comparison QCMerger.xml @ 13:fbf1dfad22ce draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:01:48 +0000
parents 786873b9c3e3
children 86a29d233856
comparison
equal deleted inserted replaced
12:f9d1fac71776 13:fbf1dfad22ce
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="QCMerger" name="QCMerger" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="QCMerger" name="QCMerger" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Merges two qcml files together.</description> 5 <description>Merges two qcml files together.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">QCMerger</token> 7 <token name="@EXECUTABLE@">QCMerger</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($in_cond.in.ext)' &&
23 #end if
21 mkdir out && 24 mkdir out &&
22 25
23 ## Main program call 26 ## Main program call
24 27
25 set -o pipefail && 28 set -o pipefail &&
26 @EXECUTABLE@ -write_ctd ./ && 29 @EXECUTABLE@ -write_ctd ./ &&
27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && 30 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd 31 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
29 -in 32 -in
30 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} 33 #if $in_cond.in_select == "no"
34 ${' '.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])}
35 #else
36 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
37 #end if
31 -out 38 -out
32 'out/output.${gxy2omsext("qcml")}' 39 'out/output.${gxy2omsext("qcml")}'
33 40
34 ## Postprocessing 41 ## Postprocessing
35 && mv 'out/output.${gxy2omsext("qcml")}' '$out' 42 && mv 'out/output.${gxy2omsext("qcml")}' '$out'
39 <configfiles> 46 <configfiles>
40 <inputs name="args_json" data_style="paths"/> 47 <inputs name="args_json" data_style="paths"/>
41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 48 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
42 </configfiles> 49 </configfiles>
43 <inputs> 50 <inputs>
44 <param name="in" argument="-in" type="data" format="qcml" multiple="true" optional="false" label="List of qcml files to be merged" help=" select qcml data sets(s)"/> 51 <conditional name="in_cond">
45 <param name="setname" 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=""> 52 <param name="in_select" type="select" label="Run tool in batch mode for -in">
46 <expand macro="list_string_san"/> 53 <option value="no">No: process all datasets jointly</option>
54 <option value="yes">Yes: process each dataset in an independent job</option>
55 </param>
56 <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)"/>
58 </when>
59 <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)"/>
61 </when>
62 </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="">
64 <expand macro="list_string_san" name="setname"/>
47 </param> 65 </param>
48 <expand macro="adv_opts_macro"> 66 <expand macro="adv_opts_macro">
49 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 67 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
50 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 68 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
51 <expand macro="list_string_san"/> 69 <expand macro="list_string_san" name="test"/>
52 </param> 70 </param>
53 </expand> 71 </expand>
54 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 72 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
55 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 73 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
56 </param> 74 </param>
59 <data name="out" label="${tool.name} on ${on_string}: out" format="qcml"/> 77 <data name="out" label="${tool.name} on ${on_string}: out" format="qcml"/>
60 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 78 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
61 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 79 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
62 </data> 80 </data>
63 </outputs> 81 </outputs>
64 <tests> 82 <tests><test expect_num_outputs="1"><!-- just using 2 outputs from QCCalculator as input (no2 did not work) -->
65 <expand macro="autotest_QCMerger"/> 83 <param name="adv_opts|test" value="true"/>
66 <expand macro="manutest_QCMerger"/> 84 <param name="in" ftype="qcml" value="QCCalculator1.qcML,QCCalculator3.qcML"/>
67 </tests> 85 <output name="out" ftype="qcml" value="QCMerger.qcML"/>
86 </test>
87 </tests>
68 <help><![CDATA[Merges two qcml files together. 88 <help><![CDATA[Merges two qcml files together.
69 89
70 90
71 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_QCMerger.html]]></help> 91 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_QCMerger.html]]></help>
72 <expand macro="references"/> 92 <expand macro="references"/>
73 </tool> 93 </tool>