Mercurial > repos > galaxyp > openms_psmfeatureextractor

comparison PSMFeatureExtractor.xml @ 8:59736982ab7b draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms"
author galaxyp
date Mon, 14 Dec 2020 16:54:21 +0000
parents 151e4b119c70
children 047020d9012f
comparison
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7:db2f53435366 8:59736982ab7b
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: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="PSMFeatureExtractor" name="PSMFeatureExtractor" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="PSMFeatureExtractor" name="PSMFeatureExtractor" version="@TOOL_VERSION@+galaxy1" profile="20.05">
5 <description>Computes extra features for each input PSM.</description> 5 <description>Computes extra features for each input PSM.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">PSMFeatureExtractor</token> 7 <token name="@EXECUTABLE@">PSMFeatureExtractor</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import> 9 <import>macros_autotest.xml</import>
15 @EXT_FOO@ 15 @EXT_FOO@
16 #import re 16 #import re
17 17
18 ## Preprocessing 18 ## Preprocessing
19 mkdir in && 19 mkdir in &&
20 #if $in
20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } 21 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
22 #else if $in_single
23 ln -s '$in_single' 'in/${re.sub("[^\w\-_]", "_", $in_single.element_identifier)}.$gxy2omsext($in_single.ext)' &&
24 #end if
21 mkdir out && 25 mkdir out &&
22 26
23 ## Main program call 27 ## Main program call
24 28
25 set -o pipefail && 29 set -o pipefail &&
26 @EXECUTABLE@ -write_ctd ./ && 30 @EXECUTABLE@ -write_ctd ./ &&
27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && 31 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd 32 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
29 -in 33 -in
34 #if $in
30 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} 35 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
36 #else if $in_single
37 'in/${re.sub("[^\w\-_]", "_", $in_single.element_identifier)}.$gxy2omsext($in_single.ext)' &&
38 #end if
31 -out 39 -out
32 'out/output.${out_type}' 40 'out/output.${out_type}'
33 41
34 ## Postprocessing 42 ## Postprocessing
35 && mv 'out/output.${out_type}' '$out' 43 && mv 'out/output.${out_type}' '$out'
39 <configfiles> 47 <configfiles>
40 <inputs name="args_json" data_style="paths"/> 48 <inputs name="args_json" data_style="paths"/>
41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 49 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
42 </configfiles> 50 </configfiles>
43 <inputs> 51 <inputs>
44 <param name="in" argument="-in" type="data" format="idxml,mzid" multiple="true" optional="false" label="Input file(s)" help=" select idxml,mzid data sets(s)"/> 52 <param name="in_single" argument="-in" type="data" format="idxml,mzid" multiple="false" optional="true" label="Input file for batch processing" help="(exactly one of -in or -in_list is required)"/>
53 <param name="in" argument="-in" type="data" format="idxml,mzid" multiple="true" optional="true" label="Input file(s) for joint processing" help="(exactly one of -in or -in_list is required)"/>
45 <param name="out_type" argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help=""> 54 <param name="out_type" argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="">
46 <option value="idXML">idxml</option> 55 <option value="idXML">idxml</option>
47 <option value="mzid">mzid</option> 56 <option value="mzid">mzid</option>
48 <expand macro="list_string_san"/> 57 <expand macro="list_string_san"/>
49 </param> 58 </param>