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Fix DIA-NN #736

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Nov 30, 2023
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26 changes: 24 additions & 2 deletions tools/diann/diann.xml
Original file line number Diff line number Diff line change
Expand Up @@ -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@">1</token>
<token name="@VERSION_SUFFIX@">2</token>
</macros>
<requirements>
<container type="docker">biocontainers/diann:v@TOOL_VERSION@_cv1</container>
Expand All @@ -29,13 +29,17 @@
#set $fasta_file_str += '--fasta ' + str($fasta_file) + ' '
#end for

#if $input.spectral_lib_options.lib
ln -s '$input.spectral_lib_options.lib' './input_data/report-lib.predicted.speclib' &&
#end if

diann
#if $input.f != 'None'
'$infiles_str'
#end if
--dir ./
#if $input.spectral_lib_options.lib
--lib '$input.spectral_lib_options.lib'
--lib './input_data/report-lib.predicted.speclib'
#else
--lib
#end if
Expand Down Expand Up @@ -464,6 +468,24 @@
</assert_contents>
</output>
</test>
<!-- test for spec library -->
<test expect_num_outputs="1">
<section name="input">
<param name="f" value="small-peakpicking-cwt-allMS.mzML" />
<section name="spectral_lib_options">
<param name="lib" value="report-lib.predicted.speclib"/>
</section>
<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">-->
<!-- <section name="input">-->
Expand Down