Update diann (#729)

* Raise version

* Add option to load multiple FASTA files

* Add new test for multi-fasta

* Fix report.tsv not found when only speclib is generated

* Update test with speclib outputs

* Add speclib files to output

* Fix test and add test-data

* Fix for diann in docker

* Test datatype issue

* Test datatype

* Test datatype issue

* Test datatype issue

* Test datatype issue

* Test datatype issue

tools/diann/diann.xml

@@ -2,7 +2,7 @@
     <description>is a software for DIA/SWATH data processing</description>
     <macros>
         <token name="@TOOL_VERSION@">1.8.1</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <requirements>
         <container type="docker">biocontainers/diann:v@TOOL_VERSION@_cv1</container>
@@ -24,8 +24,13 @@
             #end if
         #end for
 
+        #set $fasta_file_str = ''
+        #for $fasta_file in $input.fasta_db_options.fasta
+            #set $fasta_file_str += '--fasta ' + str($fasta_file) + ' '
+        #end for
+
         diann
-            #if len($input.f) > 0
+            #if $input.f != 'None'
             '$infiles_str'
             #end if
             --dir ./
@@ -34,7 +39,9 @@
             #else
             --lib
             #end if
+            #if $input.f != 'None'
             --out ./report.tsv
+            #end if
             #if $input.spectral_lib_options.gen_spec_lib
             --out-lib ./report-lib.tsv
             #end if
@@ -58,7 +65,9 @@
             #end if
 
             ## FASTA database options
-            --fasta '$input.fasta_db_options.fasta'
+            #if $fasta_file_str != 'None'
+            '$fasta_file_str'
+            #end if
             #if $input.fasta_db_options.fasta_filter
             --fasta-filter '$input.fasta_db_options.fasta_filter'
             #end if
@@ -218,6 +227,8 @@
 
             #if $input.spectral_lib_options.gen_spec_lib
             && cp ./report-lib.tsv '$output_report_lib'
+            && cp ./report-lib.tsv.speclib '$output_report_speclib'
+            && cp ./report-lib.predicted.speclib '$output_report_pred_speclib'
             #end if
     ]]></command>
     <inputs>
@@ -238,7 +249,7 @@
             </section>
             <section name="fasta_db_options" title="FASTA database">
                 <!-- ToDo fasta: use multiple fasta commands to specify multiple databases -->
-                <param name="fasta" type="data" format="fasta" label="Sequence database" help="Specify a sequence database in FASTA format"/>
+                <param name="fasta" type="data" format="fasta" multiple="true" label="Sequence database" help="Specify a sequence database in FASTA format"/>
                 <param name="fasta_filter" type="data" format="txt" optional="true" label="Fasta filter" help="Only consider peptides matching the stripped sequences specified in the text file provided, when processing a sequence database"/>
                 <param name="fasta_search" type="boolean" truevalue="--fasta-search" falsevalue="" checked="false" label="Perform in silico digest of the sequence database" help="Instructs DIA-NN to perform an in silico digest of the sequence database"/>
             </section>
@@ -399,15 +410,21 @@
     </inputs>
     <outputs>
         <data format="tabular" name="output_report" label="${tool.name} on ${on_string}: report.tsv">
-            <filter>len(input['f']) > 0</filter>
+            <filter>input['f'] != None</filter>
         </data>
         <data format="tabular" name="output_report_lib" label="${tool.name} on ${on_string}: report-lib.tsv">
             <filter>input['spectral_lib_options']['gen_spec_lib'] == True</filter>
         </data>
+        <data format="data" name="output_report_speclib" label="${tool.name} on ${on_string}: report-lib.tsv.speclib">
+            <filter>input['spectral_lib_options']['gen_spec_lib'] == True</filter>
+        </data>
+        <data format="data" name="output_report_pred_speclib" label="${tool.name} on ${on_string}: report-lib.predicted.speclib">
+            <filter>input['spectral_lib_options']['gen_spec_lib'] == True</filter>
+        </data>
     </outputs>
     <tests>
         <!-- test for default run -->
-        <test expect_num_outputs="2">
+        <test expect_num_outputs="4">
             <section name="input">
                 <param name="f" value="small-peakpicking-cwt-allMS.mzML" />
                 <section name="spectral_lib_options">
@@ -429,6 +446,23 @@
                     <has_text text="PrecursorMz"/>
                 </assert_contents>
             </output>
+            <output name="output_report_speclib" file="report-lib.tsv.speclib" compare="sim_size" delta="100"/>
+            <output name="output_report_pred_speclib" file="report-lib.predicted.speclib" compare="sim_size" delta="100"/>
+        </test>
+        <!-- test for multiple fastas -->
+        <test expect_num_outputs="1">
+            <section name="input">
+                <param name="f" value="small-peakpicking-cwt-allMS.mzML" />
+                <section name="fasta_db_options">
+                    <param name="fasta" value="bsa.fasta,bsa2.fasta"/>
+                    <param name="fasta_search" value="True"/>
+                </section>
+            </section>
+            <output name="output_report" file="report.tsv">
+                <assert_contents>
+                    <has_text text="PG.Normalised"/>
+                </assert_contents>
+            </output>
         </test>
         <!-- test for Bruker data -->
 <!--        <test expect_num_outputs="2">-->

tools/diann/test-data/bsa2.fasta

@@ -0,0 +1,7 @@
+>bsa_test sp|P02769|ALBU_BOVIN_TEST Serum albumin OS=Bos taurus OX=9913 GN=ALB PE=1 SV=4
+MKWVTFISLLLLFSSAYSRGVFRRDTHKSEIAHRFKDLGEEHFKGLVLIAFSQYLQQCPF
+DEHVKLVNELTEFAEDKDVCKNYQEAKDAFLGSFLYEYSRRHLVDEPQNLIKQNCDQFEK
+HPEYAVSVLLRLAKEYEATLEECCAKDDPHACYSTVFDKLKHLVDEPQNLIKQNCDQFEK
+LGEYGFQNALIVRYTRKVPQVSTPTLVEVSRSLGKVGTRCCTKPESERMPCTEDYLSLIL
+NRLCVLHEKTPVSEKVTDTEKQIKKQTALVELLKHKPKATEEQLKTVMENFVAFVDKCCA
+STQTALA