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comparison diann.xml @ 2:bf0728e000cd draft

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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
comparison
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1:ae4dc0c041f9 2:bf0728e000cd
1 <tool id="diann" name="DIA-NN" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="diann" name="DIA-NN" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>is a software for DIA/SWATH data processing</description> 2 <description>is a software for DIA/SWATH data processing</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">1.8.1</token> 4 <token name="@TOOL_VERSION@">1.8.1</token>
5 <token name="@VERSION_SUFFIX@">1</token> 5 <token name="@VERSION_SUFFIX@">2</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <container type="docker">biocontainers/diann:v@TOOL_VERSION@_cv1</container> 8 <container type="docker">biocontainers/diann:v@TOOL_VERSION@_cv1</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
27 #set $fasta_file_str = '' 27 #set $fasta_file_str = ''
28 #for $fasta_file in $input.fasta_db_options.fasta 28 #for $fasta_file in $input.fasta_db_options.fasta
29 #set $fasta_file_str += '--fasta ' + str($fasta_file) + ' ' 29 #set $fasta_file_str += '--fasta ' + str($fasta_file) + ' '
30 #end for 30 #end for
31 31
32 #if $input.spectral_lib_options.lib
33 ln -s '$input.spectral_lib_options.lib' './input_data/report-lib.predicted.speclib' &&
34 #end if
35
32 diann 36 diann
33 #if $input.f != 'None' 37 #if $input.f != 'None'
34 '$infiles_str' 38 '$infiles_str'
35 #end if 39 #end if
36 --dir ./ 40 --dir ./
37 #if $input.spectral_lib_options.lib 41 #if $input.spectral_lib_options.lib
38 --lib '$input.spectral_lib_options.lib' 42 --lib './input_data/report-lib.predicted.speclib'
39 #else 43 #else
40 --lib 44 --lib
41 #end if 45 #end if
42 #if $input.f != 'None' 46 #if $input.f != 'None'
43 --out ./report.tsv 47 --out ./report.tsv
462 <assert_contents> 466 <assert_contents>
463 <has_text text="PG.Normalised"/> 467 <has_text text="PG.Normalised"/>
464 </assert_contents> 468 </assert_contents>
465 </output> 469 </output>
466 </test> 470 </test>
471 <!-- test for spec library -->
472 <test expect_num_outputs="1">
473 <section name="input">
474 <param name="f" value="small-peakpicking-cwt-allMS.mzML" />
475 <section name="spectral_lib_options">
476 <param name="lib" value="report-lib.predicted.speclib"/>
477 </section>
478 <section name="fasta_db_options">
479 <param name="fasta" value="bsa.fasta,bsa2.fasta"/>
480 <param name="fasta_search" value="True"/>
481 </section>
482 </section>
483 <output name="output_report" file="report.tsv">
484 <assert_contents>
485 <has_text text="PG.Normalised"/>
486 </assert_contents>
487 </output>
488 </test>
467 <!-- test for Bruker data --> 489 <!-- test for Bruker data -->
468 <!-- <test expect_num_outputs="2">--> 490 <!-- <test expect_num_outputs="2">-->
469 <!-- <section name="input">--> 491 <!-- <section name="input">-->
470 <!-- <param name="f" value="ThyroglobMRM000003.d.tar" />--> 492 <!-- <param name="f" value="ThyroglobMRM000003.d.tar" />-->
471 <!-- <section name="spectral_lib_options">--> 493 <!-- <section name="spectral_lib_options">-->