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comparison OpenSwathFeatureXMLToTSV.xml @ 12:844c32358954 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 19:21:34 +0000
parents 5c50095229a5
children 604c9363dcfd
comparison
equal deleted inserted replaced
11:72e4bf868316 12:844c32358954
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: [Targeted Experiments]--> 3 <!--Proposed Tool Section: [Targeted Experiments]-->
4 <tool id="OpenSwathFeatureXMLToTSV" name="OpenSwathFeatureXMLToTSV" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="OpenSwathFeatureXMLToTSV" name="OpenSwathFeatureXMLToTSV" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Converts a featureXML to a mProphet tsv.</description> 5 <description>Converts a featureXML to a mProphet tsv.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">OpenSwathFeatureXMLToTSV</token> 7 <token name="@EXECUTABLE@">OpenSwathFeatureXMLToTSV</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_cond.in &&
20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } 18 #if $in_cond.in_select == "no"
19 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
20 ${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
21 #else
22 ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
23 #end if
21 mkdir tr && 24 mkdir tr &&
22 ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' && 25 ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
23 mkdir out && 26 mkdir out &&
24 27
25 ## Main program call 28 ## Main program call
27 set -o pipefail && 30 set -o pipefail &&
28 @EXECUTABLE@ -write_ctd ./ && 31 @EXECUTABLE@ -write_ctd ./ &&
29 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && 32 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
30 @EXECUTABLE@ -ini @EXECUTABLE@.ctd 33 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
31 -in 34 -in
32 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} 35 #if $in_cond.in_select == "no"
36 ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
37 #else
38 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
39 #end if
33 -tr 40 -tr
34 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' 41 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)'
35 -out 42 -out
36 'out/output.${gxy2omsext("csv")}' 43 'out/output.${gxy2omsext("csv")}'
37 44
43 <configfiles> 50 <configfiles>
44 <inputs name="args_json" data_style="paths"/> 51 <inputs name="args_json" data_style="paths"/>
45 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 52 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
46 </configfiles> 53 </configfiles>
47 <inputs> 54 <inputs>
48 <param name="in" argument="-in" type="data" format="featurexml" multiple="true" optional="false" label="Input files separated by blank" help=" select featurexml data sets(s)"/> 55 <conditional name="in_cond">
49 <param name="tr" argument="-tr" type="data" format="traml" optional="false" label="TraML transition file" help=" select traml data sets(s)"/> 56 <param name="in_select" type="select" label="Run tool in batch mode for -in">
50 <param name="short_format" argument="-short_format" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to write short (one peptide per line) or long format (one transition per line)" help=""/> 57 <option value="no">No: process all datasets jointly</option>
51 <param name="best_scoring_peptide" argument="-best_scoring_peptide" type="text" optional="true" value="" label="If only the best scoring feature per peptide should be printed, give the variable name" help=""> 58 <option value="yes">Yes: process each dataset in an independent job</option>
52 <expand macro="list_string_san"/> 59 </param>
60 <when value="no">
61 <param argument="-in" type="data" format="featurexml" multiple="true" optional="false" label="Input files separated by blank" help=" select featurexml data sets(s)"/>
62 </when>
63 <when value="yes">
64 <param argument="-in" type="data" format="featurexml" multiple="false" optional="false" label="Input files separated by blank" help=" select featurexml data sets(s)"/>
65 </when>
66 </conditional>
67 <param argument="-tr" type="data" format="traml" optional="false" label="TraML transition file" help=" select traml data sets(s)"/>
68 <param argument="-short_format" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to write short (one peptide per line) or long format (one transition per line)" help=""/>
69 <param argument="-best_scoring_peptide" type="text" optional="true" value="" label="If only the best scoring feature per peptide should be printed, give the variable name" help="">
70 <expand macro="list_string_san" name="best_scoring_peptide"/>
53 </param> 71 </param>
54 <expand macro="adv_opts_macro"> 72 <expand macro="adv_opts_macro">
55 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 73 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
56 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 74 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
57 <expand macro="list_string_san"/> 75 <expand macro="list_string_san" name="test"/>
58 </param> 76 </param>
59 </expand> 77 </expand>
60 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 78 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
61 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 79 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
62 </param> 80 </param>
65 <data name="out" label="${tool.name} on ${on_string}: out" format="csv"/> 83 <data name="out" label="${tool.name} on ${on_string}: out" format="csv"/>
66 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 84 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
67 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 85 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
68 </data> 86 </data>
69 </outputs> 87 </outputs>
70 <tests> 88 <tests><!-- TOPP_OpenSwathFeatureXMLToTSV_test_1 -->
71 <expand macro="autotest_OpenSwathFeatureXMLToTSV"/> 89 <test expect_num_outputs="2">
72 <expand macro="manutest_OpenSwathFeatureXMLToTSV"/> 90 <section name="adv_opts">
91 <param name="force" value="false"/>
92 <param name="test" value="true"/>
93 </section>
94 <conditional name="in_cond">
95 <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
96 </conditional>
97 <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
98 <output name="out" file="OpenSwathFeatureXMLToTSV_output.short.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
99 <param name="short_format" value="true"/>
100 <param name="best_scoring_peptide" value=""/>
101 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
102 <output name="ctd_out" ftype="xml">
103 <assert_contents>
104 <is_valid_xml/>
105 </assert_contents>
106 </output>
107 </test>
108 <!-- TOPP_OpenSwathFeatureXMLToTSV_test_2 -->
109 <test expect_num_outputs="2">
110 <section name="adv_opts">
111 <param name="force" value="false"/>
112 <param name="test" value="true"/>
113 </section>
114 <conditional name="in_cond">
115 <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
116 </conditional>
117 <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
118 <output name="out" file="OpenSwathFeatureXMLToTSV_output.long.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
119 <param name="short_format" value="false"/>
120 <param name="best_scoring_peptide" value=""/>
121 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
122 <output name="ctd_out" ftype="xml">
123 <assert_contents>
124 <is_valid_xml/>
125 </assert_contents>
126 </output>
127 </test>
128 <!-- TOPP_OpenSwathFeatureXMLToTSV_test_3 -->
129 <test expect_num_outputs="2">
130 <section name="adv_opts">
131 <param name="force" value="false"/>
132 <param name="test" value="true"/>
133 </section>
134 <conditional name="in_cond">
135 <param name="in" value="OpenSwathFeatureXMLToTSV_input.featureXML"/>
136 </conditional>
137 <param name="tr" value="OpenSwathFeatureXMLToTSV_input.TraML"/>
138 <output name="out" file="OpenSwathFeatureXMLToTSV_3_output.short.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
139 <param name="short_format" value="true"/>
140 <param name="best_scoring_peptide" value="main_var_xx_lda_prelim_score"/>
141 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
142 <output name="ctd_out" ftype="xml">
143 <assert_contents>
144 <is_valid_xml/>
145 </assert_contents>
146 </output>
147 </test>
73 </tests> 148 </tests>
74 <help><![CDATA[Converts a featureXML to a mProphet tsv. 149 <help><![CDATA[Converts a featureXML to a mProphet tsv.
75 150
76 151
77 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_OpenSwathFeatureXMLToTSV.html]]></help> 152 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_OpenSwathFeatureXMLToTSV.html]]></help>
78 <expand macro="references"/> 153 <expand macro="references"/>
79 </tool> 154 </tool>