Mercurial > repos > galaxyp > openms_idmerger

comparison IDMerger.xml @ 11:64dbb1eb0048 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 12:42:07 +0000
parents 763da682fd1f
children 978de6b97ca8
comparison
equal deleted inserted replaced
10:8d4db262964c 11:64dbb1eb0048
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [File Handling]--> 3 <!--Proposed Tool Section: [File Handling]-->
4 <tool id="IDMerger" name="IDMerger" version="2.3.0"> 4 <tool id="IDMerger" name="IDMerger" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Merges several protein/peptide identification files into one file.</description> 5 <description>Merges several protein/peptide identification files into one file.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">IDMerger</token> 7 <token name="@EXECUTABLE@">IDMerger</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[IDMerger 15 @EXT_FOO@
16 #import re
14 17
15 -in 18 ## Preprocessing
16 #if $merge.select_merge == 'single': 19 mkdir in &&
17 #for $token in $merge.param_in: 20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
18 $token 21 mkdir out &&
19 #end for 22 #if $add_to:
20 #else: 23 mkdir add_to &&
21 #for $token in $merge.inputs: 24 ln -s '$add_to' 'add_to/${re.sub("[^\w\-_]", "_", $add_to.element_identifier)}.$gxy2omsext($add_to.ext)' &&
22 $token.param_in
23 #end for
24 #end if 25 #end if
25 26
26 #if $param_out: 27 ## Main program call
27 -out $param_out 28
29 set -o pipefail &&
30 @EXECUTABLE@ -write_ctd ./ &&
31 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
32 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
33 -in
34 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
35 -out
36 'out/output.${gxy2omsext("idxml")}'
37 #if $add_to:
38 -add_to
39 'add_to/${re.sub("[^\w\-_]", "_", $add_to.element_identifier)}.$gxy2omsext($add_to.ext)'
28 #end if 40 #end if
29 #if $param_add_to: 41
30 -add_to $param_add_to 42 ## Postprocessing
31 #end if 43 && mv 'out/output.${gxy2omsext("idxml")}' '$out'
32 #if $param_annotate_file_origin: 44 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
33 -annotate_file_origin 45 && mv '@EXECUTABLE@.ctd' '$ctd_out'
34 #end if 46 #end if]]></command>
35 #if $param_pepxml_protxml: 47 <configfiles>
36 -pepxml_protxml 48 <inputs name="args_json" data_style="paths"/>
37 #end if 49 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
38 #if $adv_opts.adv_opts_selector=='advanced': 50 </configfiles>
39 #if $adv_opts.param_force:
40 -force
41 #end if
42 #end if
43 ]]></command>
44 <inputs> 51 <inputs>
45 52 <param name="in" argument="-in" type="data" format="idxml" multiple="true" optional="false" label="Input files separated by blanks" help=" select idxml data sets(s)"/>
46 <conditional name="merge"> 53 <param name="add_to" argument="-add_to" type="data" format="idxml" optional="true" label="Optional input file" help="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) select idxml data sets(s)"/>
47 <param help="" label="Reduce collections" name="select_merge" type="select"> 54 <param name="annotate_file_origin" argument="-annotate_file_origin" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Store the original filename in each protein/peptide identification (meta value: file_origin)" help=""/>
48 <option selected="True" value="single">Reduce collections into one file</option> 55 <param name="pepxml_protxml" argument="-pepxml_protxml" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Merge idXML files derived from a pepXML and corresponding protXML file" help="Exactly two input files are expected in this case. Not compatible with 'add_to'"/>
49 <option value="repeat">Reduce collections, by aggregating single files of multiple collections</option> 56 <param name="merge_proteins_add_PSMs" argument="-merge_proteins_add_PSMs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Merge all identified proteins by accession into one protein identification run but keep all the PSMs with updated links to potential new protein ID#s" help="Not compatible with 'add_to'"/>
50 </param> 57 <expand macro="adv_opts_macro">
51 <when value="single"> 58 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
52 <param name="param_in" type="data" multiple="True" format="idxml" label="Input files separated by blanks" help="(-in) "/> 59 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
53 </when> 60 <expand macro="list_string_san"/>
54 <when value="repeat"> 61 </param>
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
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)"/>
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) "/>
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'"/>
64 <expand macro="advanced_options">
65 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
66 </expand> 62 </expand>
63 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
64 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
65 </param>
67 </inputs> 66 </inputs>
68 <outputs> 67 <outputs>
69 <data name="param_out" format="idxml"/> 68 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
69 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
70 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
71 </data>
70 </outputs> 72 </outputs>
71 <help>Merges several protein/peptide identification files into one file. 73 <tests>
74 <expand macro="autotest_IDMerger"/>
75 <expand macro="manutest_IDMerger"/>
76 </tests>
77 <help><![CDATA[Merges several protein/peptide identification files into one file.
72 78
73 79
74 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_IDMerger.html</help> 80 For more information, visit http://www.openms.de/documentation/TOPP_IDMerger.html]]></help>
81 <expand macro="references"/>
75 </tool> 82 </tool>