Mercurial > repos > galaxyp > openms_qcmerger

comparison QCMerger.xml @ 14:86a29d233856 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:35:44 +0000
parents fbf1dfad22ce
children
comparison
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13:fbf1dfad22ce 14:86a29d233856
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.--> 1 <!--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]--> 2 <!--Proposed Tool Section: []-->
4 <tool id="QCMerger" name="QCMerger" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="QCMerger" name="QCMerger" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Merges two qcml files together.</description> 4 <description>Merges two qcml files together</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">QCMerger</token> 6 <token name="@EXECUTABLE@">QCMerger</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in_cond.in && 16 mkdir in_cond.in &&
18 #if $in_cond.in_select == "no" 17 #if $in_cond.in_select == "no"
19 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 18 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])} 19 ${' '.join(["cp '%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 20 #else
22 ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' && 21 cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
23 #end if 22 #end if
24 mkdir out && 23 mkdir out &&
25 24
26 ## Main program call 25 ## Main program call
27 26
52 <param name="in_select" type="select" label="Run tool in batch mode for -in"> 51 <param name="in_select" type="select" label="Run tool in batch mode for -in">
53 <option value="no">No: process all datasets jointly</option> 52 <option value="no">No: process all datasets jointly</option>
54 <option value="yes">Yes: process each dataset in an independent job</option> 53 <option value="yes">Yes: process each dataset in an independent job</option>
55 </param> 54 </param>
56 <when value="no"> 55 <when value="no">
57 <param argument="-in" type="data" format="qcml" multiple="true" optional="false" label="List of qcml files to be merged" help=" select qcml data sets(s)"/> 56 <param argument="-in" type="data" format="qcml" multiple="true" label="List of qcml files to be merged" help=" select qcml data sets(s)"/>
58 </when> 57 </when>
59 <when value="yes"> 58 <when value="yes">
60 <param argument="-in" type="data" format="qcml" multiple="false" optional="false" label="List of qcml files to be merged" help=" select qcml data sets(s)"/> 59 <param argument="-in" type="data" format="qcml" label="List of qcml files to be merged" help=" select qcml data sets(s)"/>
61 </when> 60 </when>
62 </conditional> 61 </conditional>
63 <param argument="-setname" type="text" optional="true" value="" label="Use only when all given qcml files belong to one set, which will be held under the given name" help=""> 62 <param argument="-setname" type="text" optional="true" value="" label="Use only when all given qcml files belong to one set, which will be held under the given name" help="">
64 <expand macro="list_string_san" name="setname"/> 63 <expand macro="list_string_san" name="setname"/>
65 </param> 64 </param>
66 <expand macro="adv_opts_macro"> 65 <expand macro="adv_opts_macro">
67 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 66 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
68 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 67 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
69 <expand macro="list_string_san" name="test"/> 68 <expand macro="list_string_san" name="test"/>
70 </param> 69 </param>
71 </expand> 70 </expand>
72 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 71 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
73 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 72 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
77 <data name="out" label="${tool.name} on ${on_string}: out" format="qcml"/> 76 <data name="out" label="${tool.name} on ${on_string}: out" format="qcml"/>
78 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 77 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
79 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 78 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
80 </data> 79 </data>
81 </outputs> 80 </outputs>
82 <tests><test expect_num_outputs="1"><!-- just using 2 outputs from QCCalculator as input (no2 did not work) --> 81 <tests>
83 <param name="adv_opts|test" value="true"/> 82 <test expect_num_outputs="1">
84 <param name="in" ftype="qcml" value="QCCalculator1.qcML,QCCalculator3.qcML"/> 83 <!-- just using 2 outputs from QCCalculator as input (no2 did not work) -->
85 <output name="out" ftype="qcml" value="QCMerger.qcML"/> 84 <param name="adv_opts|test" value="true"/>
86 </test> 85 <param name="in" ftype="qcml" value="QCCalculator1.qcML,QCCalculator3.qcML"/>
87 </tests> 86 <output name="out" ftype="qcml" value="QCMerger.qcML"/>
87 </test>
88 </tests>
88 <help><![CDATA[Merges two qcml files together. 89 <help><![CDATA[Merges two qcml files together.
89 90
90 91
91 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_QCMerger.html]]></help> 92 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_QCMerger.html]]></help>
92 <expand macro="references"/> 93 <expand macro="references"/>
93 </tool> 94 </tool>