Mercurial > repos > galaxyp > openms_qcmerger

annotate 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
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5cb44893d700 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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1 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
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2 <!--Proposed Tool Section: []-->
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3 <tool id="QCMerger" name="QCMerger" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Merges two qcml files together</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">QCMerger</token>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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11 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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12 @EXT_FOO@
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13 #import re
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15 ## Preprocessing
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16 mkdir in_cond.in &&
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17 #if $in_cond.in_select == "no"
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18 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
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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])}
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20 #else
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21 cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
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22 #end if
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23 mkdir out &&
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25 ## Main program call
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27 set -o pipefail &&
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28 @EXECUTABLE@ -write_ctd ./ &&
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29 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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30 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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31 -in
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32 #if $in_cond.in_select == "no"
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33 ${' '.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])}
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34 #else
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35 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
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36 #end if
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37 -out
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38 'out/output.${gxy2omsext("qcml")}'
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40 ## Postprocessing
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41 && mv 'out/output.${gxy2omsext("qcml")}' '$out'
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42 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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43 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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44 #end if]]></command>
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45 <configfiles>
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46 <inputs name="args_json" data_style="paths"/>
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47 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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48 </configfiles>
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49 <inputs>
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50 <conditional name="in_cond">
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51 <param name="in_select" type="select" label="Run tool in batch mode for -in">
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52 <option value="no">No: process all datasets jointly</option>
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53 <option value="yes">Yes: process each dataset in an independent job</option>
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54 </param>
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55 <when value="no">
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56 <param argument="-in" type="data" format="qcml" multiple="true" label="List of qcml files to be merged" help=" select qcml data sets(s)"/>
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57 </when>
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58 <when value="yes">
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59 <param argument="-in" type="data" format="qcml" label="List of qcml files to be merged" help=" select qcml data sets(s)"/>
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60 </when>
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61 </conditional>
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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="">
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63 <expand macro="list_string_san" name="setname"/>
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64 </param>
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65 <expand macro="adv_opts_macro">
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66 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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67 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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68 <expand macro="list_string_san" name="test"/>
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69 </param>
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70 </expand>
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71 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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72 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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73 </param>
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74 </inputs>
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75 <outputs>
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76 <data name="out" label="${tool.name} on ${on_string}: out" format="qcml"/>
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77 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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78 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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79 </data>
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80 </outputs>
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81 <tests>
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82 <test expect_num_outputs="1">
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83 <!-- just using 2 outputs from QCCalculator as input (no2 did not work) -->
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84 <param name="adv_opts|test" value="true"/>
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85 <param name="in" ftype="qcml" value="QCCalculator1.qcML,QCCalculator3.qcML"/>
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86 <output name="out" ftype="qcml" value="QCMerger.qcML"/>
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87 </test>
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88 </tests>
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89 <help><![CDATA[Merges two qcml files together.
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90
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91
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92 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_QCMerger.html]]></help>
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93 <expand macro="references"/>
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94 </tool>