Mercurial > repos > galaxyp > diann
diff diann.xml @ 2:bf0728e000cd draft
planemo upload for repository https://github.com/vdemichev/DiaNN commit 3ff8be11f0be7b9ea486577896ded0a806d9d7ee
| author | galaxyp |
|---|---|
| date | Thu, 30 Nov 2023 09:41:52 +0000 |
| parents | ae4dc0c041f9 |
| children | ff8c9e0e8a7b |
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--- a/diann.xml Mon Oct 02 14:15:42 2023 +0000 +++ b/diann.xml Thu Nov 30 09:41:52 2023 +0000 @@ -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> @@ -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 @@ -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">-->