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comparison IDMerger.xml @ 9:763da682fd1f draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Fri, 17 May 2019 04:59:48 -0400
parents 1c87f8fc08df
children 64dbb1eb0048
comparison
equal deleted inserted replaced
8:acefdc019876 9:763da682fd1f
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
10 <expand macro="references"/> 10 <expand macro="references"/>
11 <expand macro="stdio"/> 11 <expand macro="stdio"/>
12 <expand macro="requirements"/> 12 <expand macro="requirements"/>
13 <command>IDMerger 13 <command detect_errors="aggressive"><![CDATA[IDMerger
14 14
15 -in 15 -in
16 #for token in $param_in: 16 #if $merge.select_merge == 'single':
17 $token 17 #for $token in $merge.param_in:
18 #end for 18 $token
19 #end for
20 #else:
21 #for $token in $merge.inputs:
22 $token.param_in
23 #end for
24 #end if
25
19 #if $param_out: 26 #if $param_out:
20 -out $param_out 27 -out $param_out
21 #end if 28 #end if
22 #if $param_add_to: 29 #if $param_add_to:
23 -add_to $param_add_to 30 -add_to $param_add_to
28 #if $param_pepxml_protxml: 35 #if $param_pepxml_protxml:
29 -pepxml_protxml 36 -pepxml_protxml
30 #end if 37 #end if
31 #if $adv_opts.adv_opts_selector=='advanced': 38 #if $adv_opts.adv_opts_selector=='advanced':
32 #if $adv_opts.param_force: 39 #if $adv_opts.param_force:
33 -force 40 -force
41 #end if
34 #end if 42 #end if
35 #end if 43 ]]></command>
36 </command>
37 <inputs> 44 <inputs>
38 <param name="param_in" type="data" format="idxml" multiple="true" optional="False" size="30" label="Input files separated by blanks" help="(-in) "> 45
39 <sanitizer> 46 <conditional name="merge">
40 <valid initial="string.printable"> 47 <param help="" label="Reduce collections" name="select_merge" type="select">
41 <remove value="'"/> 48 <option selected="True" value="single">Reduce collections into one file</option>
42 <remove value="&quot;"/> 49 <option value="repeat">Reduce collections, by aggregating single files of multiple collections</option>
43 </valid> 50 </param>
44 </sanitizer> 51 <when value="single">
45 </param> 52 <param name="param_in" type="data" multiple="True" format="idxml" label="Input files separated by blanks" help="(-in) "/>
53 </when>
54 <when value="repeat">
55 <repeat name="inputs" min="2" title="Input idxml files">
56 <param name="param_in" type="data" format="idxml" label="Input file" help="(-in) "/>
57 </repeat>
58 </when>
59 </conditional>
60
46 <param name="param_add_to" type="data" format="idxml" optional="True" label="Optional input file" help="(-add_to) IDs from 'in' are added to this file, but only if the (modified) peptide sequences are not present yet (considering only best hits per spectrum)"/> 61 <param name="param_add_to" type="data" format="idxml" optional="True" label="Optional input file" help="(-add_to) IDs from 'in' are added to this file, but only if the (modified) peptide sequences are not present yet (considering only best hits per spectrum)"/>
47 <param name="param_annotate_file_origin" display="radio" type="boolean" truevalue="-annotate_file_origin" falsevalue="" checked="false" optional="True" label="Store the original filename in each protein/peptide identification (meta value: file_origin)" help="(-annotate_file_origin) "/> 62 <param name="param_annotate_file_origin" display="radio" type="boolean" truevalue="-annotate_file_origin" falsevalue="" checked="false" optional="True" label="Store the original filename in each protein/peptide identification (meta value: file_origin)" help="(-annotate_file_origin) "/>
48 <param name="param_pepxml_protxml" display="radio" type="boolean" truevalue="-pepxml_protxml" falsevalue="" checked="false" optional="True" label="Merge idXML files derived from a pepXML and corresponding protXML file" help="(-pepxml_protxml) &lt;br&gt;Exactly two input files are expected in this case. Not compatible with 'add_to'"/> 63 <param name="param_pepxml_protxml" display="radio" type="boolean" truevalue="-pepxml_protxml" falsevalue="" checked="false" optional="True" label="Merge idXML files derived from a pepXML and corresponding protXML file" help="(-pepxml_protxml) &lt;br&gt;Exactly two input files are expected in this case. Not compatible with 'add_to'"/>
49 <expand macro="advanced_options"> 64 <expand macro="advanced_options">
50 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 65 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
54 <data name="param_out" format="idxml"/> 69 <data name="param_out" format="idxml"/>
55 </outputs> 70 </outputs>
56 <help>Merges several protein/peptide identification files into one file. 71 <help>Merges several protein/peptide identification files into one file.
57 72
58 73
59 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDMerger.html</help> 74 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_IDMerger.html</help>
60 </tool> 75 </tool>