Mercurial > repos > galaxyp > openms_qcshrinker

comparison QCShrinker.xml @ 9:ccfc3e189087 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 20:13:29 +0000
parents 52720a19f8f1
children 910f1fdf039a
comparison
equal deleted inserted replaced
8:fd4184a9016b 9:ccfc3e189087
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="QCShrinker" name="QCShrinker" version="2.3.0"> 4 <tool id="QCShrinker" name="QCShrinker" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report.</description> 5 <description>This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">QCShrinker</token> 7 <token name="@EXECUTABLE@">QCShrinker</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[QCShrinker 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_in: 18 ## Preprocessing
16 -in $param_in 19 mkdir in &&
20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
21 #if $run:
22 mkdir run &&
23 ln -s '$run' 'run/${re.sub("[^\w\-_]", "_", $run.element_identifier)}.$gxy2omsext($run.ext)' &&
17 #end if 24 #end if
25 mkdir out &&
18 26
19 #if $rep_param_qp_accessions: 27 ## Main program call
20 -qp_accessions 28
21 #for token in $rep_param_qp_accessions: 29 set -o pipefail &&
22 #if " " in str(token): 30 @EXECUTABLE@ -write_ctd ./ &&
23 "$token.param_qp_accessions" 31 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
24 #else 32 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
25 $token.param_qp_accessions 33 -in
26 #end if 34 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
27 #end for 35 #if $run:
36 -run
37 'run/${re.sub("[^\w\-_]", "_", $run.element_identifier)}.$gxy2omsext($run.ext)'
28 #end if 38 #end if
29 #if $param_name: 39 -out
30 -name "$param_name" 40 'out/output.${gxy2omsext("qcml")}'
31 #end if 41
32 #if $param_run: 42 ## Postprocessing
33 -run $param_run 43 && mv 'out/output.${gxy2omsext("qcml")}' '$out'
34 #end if 44 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
35 #if $param_out: 45 && mv '@EXECUTABLE@.ctd' '$ctd_out'
36 -out $param_out 46 #end if]]></command>
37 #end if 47 <configfiles>
38 #if $adv_opts.adv_opts_selector=='advanced': 48 <inputs name="args_json" data_style="paths"/>
39 #if $adv_opts.param_force: 49 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
40 -force 50 </configfiles>
41 #end if
42 #end if
43 ]]></command>
44 <inputs> 51 <inputs>
45 <param name="param_in" type="data" format="qcml" optional="False" label="Input qcml file" help="(-in) "/> 52 <param name="in" argument="-in" type="data" format="qcml" optional="false" label="Input qcml file" help=" select qcml data sets(s)"/>
46 <repeat name="rep_param_qp_accessions" min="0" title="param_qp_accessions"> 53 <param name="qp_accessions" argument="-qp_accessions" type="text" optional="true" value="" label="A list of cv accessions that should be removed" help="If empty, the usual suspects will be removed! (space separated list, in order to allow for spaces in list items surround them by single quotes)">
47 <param name="param_qp_accessions" type="text" size="30" label="A list of cv accessions that should be removed" help="(-qp_accessions) If empty, the usual suspects will be removed!"> 54 <expand macro="list_string_val"/>
48 <sanitizer> 55 <expand macro="list_string_san"/>
49 <valid initial="string.printable"> 56 </param>
50 <remove value="'"/> 57 <param name="name" argument="-name" type="text" optional="true" value="" label="The name of the target run or set that contains the requested quality paramete" help="">
51 <remove value="&quot;"/> 58 <expand macro="list_string_san"/>
52 </valid> 59 </param>
53 </sanitizer> 60 <param name="run" argument="-run" type="data" format="mzml" optional="true" label="The file from which the name of the target run that contains the requested quality parameter is taken" help="This overrides the name parameter! select mzml data sets(s)"/>
61 <expand macro="adv_opts_macro">
62 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
63 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
64 <expand macro="list_string_san"/>
54 </param> 65 </param>
55 </repeat> 66 </expand>
56 <param name="param_name" type="text" size="30" label="The name of the target run or set that contains the requested quality paramete" help="(-name) "> 67 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
57 <sanitizer> 68 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
58 <valid initial="string.printable">
59 <remove value="'"/>
60 <remove value="&quot;"/>
61 </valid>
62 </sanitizer>
63 </param> 69 </param>
64 <param name="param_run" type="data" format="mzml" optional="True" label="The file from which the name of the target run that contains the requested quality parameter is taken" help="(-run) This overrides the name parameter!"/>
65 <expand macro="advanced_options">
66 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
67 </expand>
68 </inputs> 70 </inputs>
69 <outputs> 71 <outputs>
70 <data name="param_out" format="qcml"/> 72 <data name="out" label="${tool.name} on ${on_string}: out" format="qcml"/>
73 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
74 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
75 </data>
71 </outputs> 76 </outputs>
72 <help>This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report. 77 <tests>
78 <expand macro="autotest_QCShrinker"/>
79 <expand macro="manutest_QCShrinker"/>
80 </tests>
81 <help><![CDATA[This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report.
73 82
74 83
75 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_QCShrinker.html</help> 84 For more information, visit http://www.openms.de/documentation/UTILS_QCShrinker.html]]></help>
85 <expand macro="references"/>
76 </tool> 86 </tool>