From fa140a9f660eab2459e21b0b637b129d7de24c02 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Tue, 10 Jan 2023 18:08:18 +0100
Subject: [PATCH] hiccorrectmatrix: is writing to input file (#4670)

* hiccorrectmatrix: is wrinting to input file

so we need to copy it

* skip from_workdir

* fix URLs

* workaround for a bug regarding parallel processing

that will be fixed in 3.7

* add missing options to CLI

see https://github.com/galaxyproject/tools-iuc/issues/4085

* more fixes:

- redundant name and argument
- 1 wrong parameter name in test
- 1 wrong option value and one missing option text

* fix duplicated output labels
---
 tools/hicexplorer/hicAggregateContacts.xml |  4 ++--
 tools/hicexplorer/hicConvertFormat.xml     | 25 ++++++++++++----------
 tools/hicexplorer/hicCorrectMatrix.xml     | 22 +++++++++----------
 tools/hicexplorer/hicCorrelate.xml         |  4 ++--
 tools/hicexplorer/hicDetectLoops.xml       |  2 +-
 tools/hicexplorer/hicDifferentialTAD.xml   |  3 ++-
 tools/hicexplorer/hicNormalize.xml         |  2 +-
 tools/hicexplorer/hicPCA.xml               |  8 +++----
 tools/hicexplorer/hicPlotMatrix.xml        |  2 +-
 tools/hicexplorer/hicPlotSVL.xml           |  2 +-
 tools/hicexplorer/hicTransform.xml         |  2 +-
 tools/hicexplorer/macros.xml               |  4 ++--
 12 files changed, 42 insertions(+), 38 deletions(-)

diff --git a/tools/hicexplorer/hicAggregateContacts.xml b/tools/hicexplorer/hicAggregateContacts.xml
index 6029cb2f44f..d9b1837a0a0 100644
--- a/tools/hicexplorer/hicAggregateContacts.xml
+++ b/tools/hicexplorer/hicAggregateContacts.xml
@@ -182,10 +182,10 @@
         <collection name="matrix_values" type="list" label="${tool.name} on ${on_string}: Matrix values">
             <discover_datasets pattern="matrix_values_(?P&lt;designation&gt;.*)\..*" directory="./" format="tabular" />
         </collection>
-        <collection name="contact_positions" type="list" label="${tool.name} on ${on_string}: Matrix values">
+        <collection name="contact_positions" type="list" label="${tool.name} on ${on_string}: Contact positions">
             <discover_datasets pattern="contact_positions_(?P&lt;designation&gt;.*)\..*" directory="./" format="tabular" />
         </collection>
-        <collection name="heatmap" type="list" label="${tool.name} on ${on_string}: Matrix values">
+        <collection name="heatmap" type="list" label="${tool.name} on ${on_string}: Heatmap">
             <discover_datasets pattern="heatmap_(?P&lt;designation&gt;.*)\..*" directory="./" format="tabular" />
         </collection>
         <data name="matrix_obs_exp_output" from_work_dir="matrix" format="h5" label="${tool.name} MATRIX on ${on_string}">
diff --git a/tools/hicexplorer/hicConvertFormat.xml b/tools/hicexplorer/hicConvertFormat.xml
index 222059aa392..554e06132ec 100644
--- a/tools/hicexplorer/hicConvertFormat.xml
+++ b/tools/hicexplorer/hicConvertFormat.xml
@@ -88,16 +88,8 @@
             --outputFormat $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector
             --outFileName 'matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector'
 
-            #if $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector == 'ginteractions':
-                && mv 'matrix.${outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector}.tsv' matrix_out
-            #else:
-                && mv 'matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector' matrix_out
-            #end if
-        #end if
-
-
         ### Set up links to matrices to have correct ending
-        #if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'multipleMatrix':
+        #else if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'multipleMatrix':
             #if $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.resolutionOrManyToOne_selector == 'resolution_option':
                 #set xml_path = $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.inputFormat_conditional
                 #if $xml_path.inputFormat_selector == 'optionCool':
@@ -206,6 +198,17 @@
                 --matrices $m
             #end if
             --outFileName matrix.mcool
+        #end if
+        $storeAppliedCorrection
+        $enforceInteger
+
+        #if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'singleMatrix':
+            #if $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector == 'ginteractions':
+                && mv 'matrix.${outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector}.tsv' matrix_out
+            #else:
+                && mv 'matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector' matrix_out
+            #end if
+        #else if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'multipleMatrix':
             && mv matrix.mcool matrix_out
         #end if
 ]]>
@@ -237,10 +240,10 @@
                         <expand macro='convertFormat_multiple_macro' />
                     </when>
                 </conditional>
-                <param name='storeAppliedCorrection' type="boolean" truevalue="yes" falsevalue="" label='Store applied correction factors in column count' />
-                <param name='enforceInteger' type="boolean" truevalue="yes" falsevalue="" label='Enforce integer for count column' />
             </when>
         </conditional>
+        <param name='storeAppliedCorrection' type="boolean" truevalue="--store_applied_correction" falsevalue="" label="Store applied correction factors in column count" help="Option only for cool input files" />
+        <param name='enforceInteger' type="boolean" truevalue="--enforce_integer" falsevalue="" label="Enforce integer for count column" help="Option only for cool input files" />
     </inputs>
     <outputs>
         <data name='output_converted_matrix' from_work_dir='matrix_out' format='cool' label='Converted matrix'>
diff --git a/tools/hicexplorer/hicCorrectMatrix.xml b/tools/hicexplorer/hicCorrectMatrix.xml
index 699f4e93406..e3d0b6e126f 100644
--- a/tools/hicexplorer/hicCorrectMatrix.xml
+++ b/tools/hicexplorer/hicCorrectMatrix.xml
@@ -6,7 +6,7 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
+        cp '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
 
         @BINARY@
             $mode.mode_selector
@@ -55,7 +55,7 @@
                 $mode.perchr
             #end if
         #if $mode.mode_selector == 'correct':
-            && mv matrix.$matrix_h5_cooler.ext matrix
+            && mv matrix.$matrix_h5_cooler.ext '$outFileName'
         #end if
 ]]>
     </command>
@@ -68,7 +68,7 @@
             </param>
             <when value="diagnostic_plot">
                 <expand macro="xMax" />
-                <param argument="--perchr" name="perchr" type="boolean" truevalue="--perchr" falsevalue="" checked="false" label="Compute statistics for each chromosome separately" />
+                <param argument="--perchr" type="boolean" truevalue="--perchr" falsevalue="" checked="false" label="Compute statistics for each chromosome separately" />
             </when>
             <when value="correct">
                 <conditional name='correctionMethod'>
@@ -78,19 +78,19 @@
                     </param>
 
                     <when value='ice'>
-                        <param argument="--iterNum" name="iterNum" type="integer" optional="true" value="500" label="Number of iterations" />
+                        <param argument="--iterNum" type="integer" optional="true" value="500" label="Number of iterations" />
 
-                        <param argument="--inflationCutoff" name="inflationCutoff" type="float" optional="true" label="Inflation cutoff" value="" help="Value corresponding to the maximum number of times a bin can be scaled up during the iterative correction.
+                        <param argument="--inflationCutoff" type="float" optional="true" label="Inflation cutoff" value="" help="Value corresponding to the maximum number of times a bin can be scaled up during the iterative correction.
                             For example, a inflationCutoff of 3 will filter out all bins that were expanded 3 times or more during the iterative correction." />
 
-                        <param argument="--transCutoff" name="transCutoff" type="float" optional="true" label="Trans region cutoff" value="" help="Clip high counts in the top -transcut trans regions (i.e. between chromosomes). A usual value is 0.05." />
+                        <param argument="--transCutoff" type="float" optional="true" label="Trans region cutoff" value="" help="Clip high counts in the top -transcut trans regions (i.e. between chromosomes). A usual value is 0.05." />
 
-                        <param argument="--sequencedCountCutoff" name="sequencedCountCutoff" optional="true" type="float" label="Sequenced count cutoff" help="Each bin receives a value indicating the fraction that is covered by reads.
+                        <param argument="--sequencedCountCutoff" optional="true" type="float" label="Sequenced count cutoff" help="Each bin receives a value indicating the fraction that is covered by reads.
                                 A cutoff of 0.5 will discard all those bins that have less than half of the bin covered." />
 
-                        <param argument="--skipDiagonal" name="skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" checked="false" label="Skip diagonal counts" />
+                        <param argument="--skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" checked="false" label="Skip diagonal counts" />
 
-                        <param argument="--perchr" name="perchr" type="boolean" truevalue="--perchr" falsevalue="" checked="false" label="Normalize each chromosome separately" />
+                        <param argument="--perchr" type="boolean" truevalue="--perchr" falsevalue="" checked="false" label="Normalize each chromosome separately" />
                         <expand macro="filterThreshold" />
                     </when>
                     <when value='kr'>
@@ -108,13 +108,13 @@
 
     </inputs>
     <outputs>
-        <data name="outFileName" from_work_dir="matrix" format="cool">
+        <data name="outFileName" format="cool">
             <change_format>
                 <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5" />
             </change_format>
             <filter>mode['mode_selector'] == "correct"</filter>
         </data>
-        <data name="diagnostic_plot" from_work_dir="diagnostic_plot.png" format="png">
+        <data name="diagnostic_plot" from_work_dir="diagnostic_plot.png" format="png" label="${tool.name} on ${on_string}: Diagnostic plot">
             <filter>mode['mode_selector'] == "diagnostic_plot"</filter>
         </data>
     </outputs>
diff --git a/tools/hicexplorer/hicCorrelate.xml b/tools/hicexplorer/hicCorrelate.xml
index 3debcb3a077..0bb54cd63d4 100644
--- a/tools/hicexplorer/hicCorrelate.xml
+++ b/tools/hicexplorer/hicCorrelate.xml
@@ -55,8 +55,8 @@
         <expand macro="colormap" />
     </inputs>
     <outputs>        <!-- not sure if argument is specifiable for output yet, would be cool if so -->
-        <data name="outFileNameHeatmap" from_work_dir="heatmap.png" format="png" />
-        <data name="outFileNameScatter" from_work_dir="scatter.png" format="png" />
+        <data name="outFileNameHeatmap" from_work_dir="heatmap.png" format="png" label="${tool.name} on ${on_string}: Heatmap"/>
+        <data name="outFileNameScatter" from_work_dir="scatter.png" format="png" label="${tool.name} on ${on_string}: Scatter plot"/>
     </outputs>
     <tests>
         <test>
diff --git a/tools/hicexplorer/hicDetectLoops.xml b/tools/hicexplorer/hicDetectLoops.xml
index a0089e6f58c..341b3c265c9 100644
--- a/tools/hicexplorer/hicDetectLoops.xml
+++ b/tools/hicexplorer/hicDetectLoops.xml
@@ -71,7 +71,7 @@
         <param argument="--expected" type="select" label="Method to compute the expected value">
             <option value="mean" selected="True">mean</option>
             <option value="mean_nonzero">mean_nonzero</option>
-            <option value="mean_nonzero">mean_nonzero_ligation</option>
+            <option value="mean_nonzero_ligation">mean_nonzero_ligation</option>
         </param>
     </inputs>
     <outputs>
diff --git a/tools/hicexplorer/hicDifferentialTAD.xml b/tools/hicexplorer/hicDifferentialTAD.xml
index a0a3f7bb31f..f606f7ba581 100644
--- a/tools/hicexplorer/hicDifferentialTAD.xml
+++ b/tools/hicexplorer/hicDifferentialTAD.xml
@@ -61,7 +61,8 @@
             <param name="mode_selector" value="all" />
             <param name="modeReject" value="one" />
             <output name="acceptedTADs" file="hicDifferentialTAD/accepted.txt" ftype="txt" />
-            <output name="rejectedTADs" file="hicDifferentialTAD/rejected.txt" ftype="txt" />
+            <!-- TODO remove lines_diff when updating to >=3.7 where" a multicore issue was solved that led to skipping data at the start and end of chromosomes-->
+            <output name="rejectedTADs" file="hicDifferentialTAD/rejected.txt" ftype="txt" lines_diff="4"/>
         </test>
     </tests>
     <help><![CDATA[
diff --git a/tools/hicexplorer/hicNormalize.xml b/tools/hicexplorer/hicNormalize.xml
index ad6a6985182..4650059e784 100644
--- a/tools/hicexplorer/hicNormalize.xml
+++ b/tools/hicexplorer/hicNormalize.xml
@@ -115,7 +115,7 @@ _________________
 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
 
 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
-.. _`Lieberman-Aiden et al. (2009)`: https://doi.org/10.1126%2Fscience.1181369
+.. _`Lieberman-Aiden et al. (2009)`: https://doi.org/10.1126/science.1181369
 ]]>    </help>
     <expand macro="citations" />
 </tool>
diff --git a/tools/hicexplorer/hicPCA.xml b/tools/hicexplorer/hicPCA.xml
index 41932b95c1e..d8b39b4046a 100644
--- a/tools/hicexplorer/hicPCA.xml
+++ b/tools/hicexplorer/hicPCA.xml
@@ -95,13 +95,13 @@
             </change_format>
         </data>
 
-        <data name="pearson_outfile" from_work_dir="pearson" format="cool">
+        <data name="pearson_outfile" from_work_dir="pearson" format="cool" label="${tool.name} on ${on_string}: Pearson matrix">
             <filter>pearsonMatrix</filter>
             <change_format>
-                <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5" />
+                <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5"/>
             </change_format>
         </data>
-        <data name="obsexp_outfile" from_work_dir="obsexp" format="cool">
+        <data name="obsexp_outfile" from_work_dir="obsexp" format="cool" label="${tool.name} on ${on_string}: observed / expected matrix">
             <filter>obsexpMatrix</filter>
             <change_format>
                 <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5" />
@@ -228,7 +228,7 @@ _________________
 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
 
 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
-.. _`Lieberman-Aiden et al. (2009)`: https://doi.org/10.1126%2Fscience.1181369
+.. _`Lieberman-Aiden et al. (2009)`: https://doi.org/10.1126/science.1181369
 ]]>    </help>
     <expand macro="citations" />
 </tool>
diff --git a/tools/hicexplorer/hicPlotMatrix.xml b/tools/hicexplorer/hicPlotMatrix.xml
index 3af39f1108a..bf98d62ab19 100644
--- a/tools/hicexplorer/hicPlotMatrix.xml
+++ b/tools/hicexplorer/hicPlotMatrix.xml
@@ -141,7 +141,7 @@
 
         <conditional name="pca_conditional">
             <param name='pca_type' label='Datatype of eigenvector file' type='select'>
-                <option value='' selected="true"></option>
+                <option value='' selected="true">None</option>
                 <option value='bigwig'>bigwig</option>
             </param>
             <when value='' />
diff --git a/tools/hicexplorer/hicPlotSVL.xml b/tools/hicexplorer/hicPlotSVL.xml
index 00ac3f02a6d..708a54e1833 100644
--- a/tools/hicexplorer/hicPlotSVL.xml
+++ b/tools/hicexplorer/hicPlotSVL.xml
@@ -66,7 +66,7 @@
             <param name="matrix_h5_cooler_multiple" value="small_test_matrix.h5,small_test_matrix.h5" />
             <param name="distance" value="2000000" />
             <param name="dpi" value="10" />
-            <param name="color" value="y m c" />
+            <param name="colorList" value="y m c" />
             <repeat name="chromosome_list">
                 <param name="chromosomes" value="chr2L" />
             </repeat>
diff --git a/tools/hicexplorer/hicTransform.xml b/tools/hicexplorer/hicTransform.xml
index dcd7aa9a863..5a163b04c1f 100644
--- a/tools/hicexplorer/hicTransform.xml
+++ b/tools/hicexplorer/hicTransform.xml
@@ -95,7 +95,7 @@ _________________
 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
 
 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
-.. _`Lieberman-Aiden et al. (2009)`: https://doi.org/10.1126%2Fscience.1181369
+.. _`Lieberman-Aiden et al. (2009)`: https://doi.org/10.1126/science.1181369
 ]]>    </help>
     <expand macro="citations" />
 </tool>
diff --git a/tools/hicexplorer/macros.xml b/tools/hicexplorer/macros.xml
index 94fdf349441..78709cdcb5d 100644
--- a/tools/hicexplorer/macros.xml
+++ b/tools/hicexplorer/macros.xml
@@ -1,7 +1,7 @@
 <macros>
     <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
     <token name="@TOOL_VERSION@">3.6</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@USE_RANGE@">
         #if $use_range.select_use_range == "yes_use_range":
             --range $use_range.range_min:$use_range.range_max
@@ -333,7 +333,7 @@
         <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)" />
     </xml>
     <xml name="xMax">
-        <param argument="--xMax" name="xMax" type="integer" optional="true" value="" label="Max value for the x-axis in counts per bin" />
+        <param argument="--xMax" type="integer" optional="true" value="" label="Max value for the x-axis in counts per bin" />
     </xml>
     <xml name="filterThreshold">
         <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5" label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect." />