Mercurial > repos > galaxyp > probamconvert

comparison probamconvert.xml @ 1:37369e255465 draft default tip

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author galaxyp
date Wed, 15 Mar 2017 09:43:14 -0400
parents 0a77e0c00146
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0:0a77e0c00146 1:37369e255465
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <exit_code range="1:" /> 7 <exit_code range="1:" />
8 </stdio> 8 </stdio>
9 <command><![CDATA[ 9 <command><![CDATA[
10 #set $psm_file = input.${input.datatype.file_ext} 10 #set $psm_file = 'input.'+str($input.datatype.file_ext)
11 ln -s "$input" $psm_file; 11 ln -s "$input" $psm_file;
12 proBAM.py --name="converted" --file=$psm_file 12 proBAM.py --name="converted" --file=$psm_file --conversion_mode=$conversion_mode
13 --database=$refsrc.database 13 --database=$refsrc.database
14 #if str($refsrc.database) == 'ENSEMBL': 14 #if str($refsrc.database) == 'ENSEMBL':
15 --species=$refsrc.species 15 --species=$refsrc.species
16 #if $refsrc.version: 16 #if $refsrc.version:
17 --version=$refsrc.version 17 --version=$refsrc.version
18 #end if 18 #end if
19 #end if 19 #end if
20 #if str($optional.decoy_annotation) != 'None': 20 #if str($optional.decoy_annotation) != '':
21 --decoy_annotation='$optional.decoy_annotation' 21 --decoy_annotation='$optional.decoy_annotation'
22 #end if 22 #end if
23 --pre_picked_annotation=$pre_picked_annotation 23 --pre_picked_annotation=$optional.pre_picked_annotation
24 --mismatches=$optional.mismatches 24 --mismatches=$optional.mismatches
25 $optional.rm_duplicates 25 $optional.rm_duplicates
26 $optional.three_frame_translation 26 $optional.three_frame_translation
27 $optional.include_unmapped 27 $optional.include_unmapped
28 --directory=outputs
29 ]]></command> 28 ]]></command>
30 <inputs> 29 <inputs>
31 <param name="input" type="data" format="mzid,pepxml" label="Peptide Indentification (mzIdentML or pepXML)"/> 30 <param name="input" type="data" format="mzid,pepxml" label="Peptide Indentification (mzIdentML or pepXML)"/>
32 <param name="conversion_mode" type="select" label="Convert to:"> 31 <param name="conversion_mode" type="select" label="Convert to:">
33 <option value="proBAM_psm">proBAM_psm</option> 32 <option value="proBAM_psm">proBAM_psm</option>
85 <option value="First">First</option> 84 <option value="First">First</option>
86 </param> 85 </param>
87 </section> 86 </section>
88 </inputs> 87 </inputs>
89 <outputs> 88 <outputs>
90 <data name="output_bam" format="pro.bam" label="" from_work_dir="outputs/converted.sorted.bam"> 89 <data name="output_bam" format="bam" label="${conversion_mode} ${input.display_name}.pro.bam" from_work_dir="converted.sorted.bam">
91 <filter>conversion_mode != 'proBED'</filter> 90 <filter>conversion_mode != 'proBED'</filter>
92 </data> 91 </data>
93 <data name="output_bed" format="pro.bed" label="" from_work_dir="outputs/converted.pro.bed"> 92 <data name="output_bed" format="bed" label="${conversion_mode} ${input.display_name}.pro.bed" from_work_dir="converted.pro.bed">
94 <filter>conversion_mode == 'proBED'</filter> 93 <filter>conversion_mode == 'proBED'</filter>
95 </data> 94 </data>
96 </outputs> 95 </outputs>
97 <tests> 96 <tests>
98 <test> 97 <test>
99 <param name="input" ftype="mzid" value="test.mzid"/> 98 <param name="input" ftype="mzid" value="test.mzid"/>
100 <param name="conversion_mode" value="proBAM_psm"/> 99 <param name="conversion_mode" value="proBED"/>
101 <param name="database" value="ENSEMBL"/> 100 <param name="database" value="ENSEMBL"/>
102 <param name="species" value="homo_sapiens"/> 101 <param name="species" value="homo_sapiens"/>
103 <param name="version" value="87"/> 102 <param name="version" value="87"/>
104 <output name="output_bam"> 103 <output name="output_bed">
105 <assert_contents> 104 <assert_contents>
106 <has_text text="Q7Z6Z7_0" /> 105 <has_text text="Q7Z6Z7_0" />
107 </assert_contents> 106 </assert_contents>
108 </output> 107 </output>
109 </test> 108 </test>