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comparison IDRipper.xml @ 13:7960e660446e draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:15:32 +0000
parents b017e7bd2316
children e64214bd2f6e
comparison
equal deleted inserted replaced
12:b577fd381b36 13:7960e660446e
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="IDRipper" name="IDRipper" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="IDRipper" name="IDRipper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Split protein/peptide identification file into several files according to annotated file origin.</description> 5 <description>Split protein/peptide identification file into several files according to identification run and annotated file origin.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">IDRipper</token> 7 <token name="@EXECUTABLE@">IDRipper</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
11 </macros> 9 </macros>
12 <expand macro="requirements"/> 10 <expand macro="requirements"/>
13 <expand macro="stdio"/> 11 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@ 13 @EXT_FOO@
16 #import re 14 #import re
17 15
18 ## Preprocessing 16 ## Preprocessing
19 mkdir in && 17 mkdir in &&
20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
21 mkdir out_path && 19 mkdir out &&
22 20
23 ## Main program call 21 ## Main program call
24 22
25 set -o pipefail && 23 set -o pipefail &&
26 @EXECUTABLE@ -write_ctd ./ && 24 @EXECUTABLE@ -write_ctd ./ &&
27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && 25 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd 26 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
29 -in 27 -in
30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' 28 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
31 -out_path 29 -out
32 out_path/ 30 out/
33 31
34 ## Postprocessing 32 ## Postprocessing
35 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS 33 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
36 && mv '@EXECUTABLE@.ctd' '$ctd_out' 34 && mv '@EXECUTABLE@.ctd' '$ctd_out'
37 #end if]]></command> 35 #end if]]></command>
38 <configfiles> 36 <configfiles>
39 <inputs name="args_json" data_style="paths"/> 37 <inputs name="args_json" data_style="paths"/>
40 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 38 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
41 </configfiles> 39 </configfiles>
42 <inputs> 40 <inputs>
43 <param name="in" argument="-in" type="data" format="idxml" optional="false" label="Input file, in which the protein/peptide identifications must be tagged with 'file_origin'" help=" select idxml data sets(s)"/> 41 <param argument="-in" type="data" format="idxml" optional="false" label="Input file, in which the protein/peptide identifications must be tagged with 'file_origin'" help=" select idxml data sets(s)"/>
42 <param argument="-numeric_filenames" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not infer output filenames from spectra_data or file_origin but use the input filename with numeric suffixes" help=""/>
43 <param argument="-split_ident_runs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Split different identification runs into separate files" help=""/>
44 <expand macro="adv_opts_macro"> 44 <expand macro="adv_opts_macro">
45 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 45 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
46 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 46 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
47 <expand macro="list_string_san"/> 47 <expand macro="list_string_san" name="test"/>
48 </param> 48 </param>
49 </expand> 49 </expand>
50 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 50 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
51 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 51 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
52 </param> 52 </param>
53 </inputs> 53 </inputs>
54 <outputs> 54 <outputs>
55 <collection type="list" name="out_path" label="${tool.name} on ${on_string}: out_path"> 55 <collection type="list" name="out" label="${tool.name} on ${on_string}: out">
56 <discover_datasets directory="out_path" format="idxml" pattern="_?(?P&lt;designation&gt;.*)\.[^.]*"/> 56 <discover_datasets directory="out" recurse="true" format="idxml" pattern="_?(?P&lt;designation&gt;.*)\.[^.]*"/>
57 </collection> 57 </collection>
58 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 58 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
59 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 59 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
60 </data> 60 </data>
61 </outputs> 61 </outputs>
62 <tests> 62 <tests><!-- TOPP_IDRipper_1 -->
63 <expand macro="autotest_IDRipper"/> 63 <!-- TOPP_IDRipper_2 -->
64 <expand macro="manutest_IDRipper"/> 64 <!-- TOPP_IDRipper_2a -->
65 </tests> 65 <!-- TOPP_IDRipper_3 -->
66 <help><![CDATA[Split protein/peptide identification file into several files according to annotated file origin. 66 <test expect_num_outputs="2">
67 <section name="adv_opts">
68 <param name="test" value="true"/>
69 </section>
70 <param name="in" value="IDRipper_1_input.idXML"/>
71 <output_collection name="out" count="2">
72 <element name="IDRipper_1_output_1" file="IDRipper_1_output1.idXML" ftype="idxml" compare="sim_size" delta="5700"/>
73 <element name="IDRipper_1_output_2" file="IDRipper_1_output2.idXML" ftype="idxml" compare="sim_size" delta="5700"/>
74 </output_collection>
75 <param name="numeric_filenames" value="false"/>
76 <param name="split_ident_runs" value="false"/>
77 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
78 <output name="ctd_out" ftype="xml">
79 <assert_contents>
80 <is_valid_xml/>
81 </assert_contents>
82 </output>
83 </test><test expect_num_outputs="2">
84 <section name="adv_opts">
85 <param name="test" value="true"/>
86 </section>
87 <param name="in" value="IDRipper_2_input.idXML"/>
88 <output_collection name="out" count="3">
89 <element name="IDRipper_2_input_idXML_0_0" file="IDRipper_2_input_0_0.idXML" ftype="idxml"/>
90 <element name="IDRipper_2_input_idXML_1_0" file="IDRipper_2_input_1_0.idXML" ftype="idxml"/>
91 <element name="IDRipper_2_input_idXML_2_1" file="IDRipper_2_input_2_1.idXML" ftype="idxml"/>
92 </output_collection>
93 <param name="numeric_filenames" value="true"/>
94 <param name="split_ident_runs" value="true"/>
95 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
96 <output name="ctd_out" ftype="xml">
97 <assert_contents>
98 <is_valid_xml/>
99 </assert_contents>
100 </output>
101 </test><test expect_num_outputs="2">
102 <section name="adv_opts">
103 <param name="test" value="true"/>
104 </section>
105 <param name="in" value="IDRipper_2_input.idXML"/>
106 <output_collection name="out" count="2">
107 <element name="IDRipper_2_input_idXML_0" file="IDRipper_2a_output_0.idXML" ftype="idxml"/>
108 <element name="IDRipper_2_input_idXML_1" file="IDRipper_2a_output_1.idXML" ftype="idxml"/>
109 </output_collection>
110 <param name="numeric_filenames" value="true"/>
111 <param name="split_ident_runs" value="false"/>
112 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
113 <output name="ctd_out" ftype="xml">
114 <assert_contents>
115 <is_valid_xml/>
116 </assert_contents>
117 </output>
118 </test><test expect_num_outputs="2">
119 <section name="adv_opts">
120 <param name="test" value="true"/>
121 </section>
122 <param name="in" value="IDRipper_3_output.idXML"/>
123 <output_collection name="out" count="2">
124 <element name="IDRipper_3_input1" file="IDRipper_3_input1.idXML" ftype="idxml"/>
125 <element name="IDRipper_3_input2" file="IDRipper_3_input2.idXML" ftype="idxml"/>
126 </output_collection>
127 <param name="numeric_filenames" value="false"/>
128 <param name="split_ident_runs" value="false"/>
129 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
130 <output name="ctd_out" ftype="xml">
131 <assert_contents>
132 <is_valid_xml/>
133 </assert_contents>
134 </output>
135 </test>
136 </tests>
137 <help><![CDATA[Split protein/peptide identification file into several files according to identification run and annotated file origin.
67 138
68 139
69 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_IDRipper.html]]></help> 140 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDRipper.html]]></help>
70 <expand macro="references"/> 141 <expand macro="references"/>
71 </tool> 142 </tool>