Mercurial > repos > galaxyp > openms_openswathmzmlfilecacher

comparison OpenSwathMzMLFileCacher.xml @ 9:e7c43d17e3dc 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 20:15:03 +0000
parents b5121b003599
children fc775d5aa321
comparison
equal deleted inserted replaced
8:05ec9fb05ed1 9:e7c43d17e3dc
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="OpenSwathMzMLFileCacher" name="OpenSwathMzMLFileCacher" version="2.3.0"> 4 <tool id="OpenSwathMzMLFileCacher" name="OpenSwathMzMLFileCacher" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>This tool caches the spectra and chromatogram data of an mzML to disk.</description> 5 <description>This tool caches the spectra and chromatogram data of an mzML to disk.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">OpenSwathMzMLFileCacher</token> 7 <token name="@EXECUTABLE@">OpenSwathMzMLFileCacher</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[OpenSwathMzMLFileCacher 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_in: 18 ## Preprocessing
16 -in $param_in 19 mkdir in &&
17 #end if 20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
18 #if $param_out: 21 mkdir out &&
19 -out $param_out 22
20 #end if 23 ## Main program call
21 #if $param_out_type: 24
22 -out_type 25 set -o pipefail &&
23 #if " " in str($param_out_type): 26 @EXECUTABLE@ -write_ctd ./ &&
24 "$param_out_type" 27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
25 #else 28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
26 $param_out_type 29 -in
27 #end if 30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
28 #end if 31 -out
29 #if $param_convert_back: 32 'out/output.${out_type}'
30 -convert_back 33
31 #end if 34 ## Postprocessing
32 #if $adv_opts.adv_opts_selector=='advanced': 35 && mv 'out/output.${out_type}' '$out'
33 #if $adv_opts.param_force: 36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
34 -force 37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
35 #end if 38 #end if]]></command>
36 #end if 39 <configfiles>
37 ]]></command> 40 <inputs name="args_json" data_style="paths"/>
41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
42 </configfiles>
38 <inputs> 43 <inputs>
39 <param name="param_in" type="data" format="mzml,sqMass" optional="False" label="Input mzML file" help="(-in) "/> 44 <param name="in" argument="-in" type="data" format="mzml,sqmass" optional="false" label="Input mzML file" help=" select mzml,sqmass data sets(s)"/>
40 <param name="param_out_type" display="radio" type="select" optional="True" label="Output file type -- default: determined from file extension or content &lt;br&gt;Note: that not all conversion paths work or make sense" help="(-out_type) "> 45 <param name="out_type" argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="Note: that not all conversion paths work or make sense">
41 <option value="mzML">mzML</option> 46 <option value="mzML">mzml</option>
42 <option value="sqMass">sqMass</option> 47 <option value="sqMass">sqmass</option>
48 <expand macro="list_string_san"/>
43 </param> 49 </param>
44 <param name="param_convert_back" display="radio" type="boolean" truevalue="-convert_back" falsevalue="" checked="false" optional="True" label="Convert back to mzML" help="(-convert_back) "/> 50 <param name="lossy_compression" argument="-lossy_compression" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use numpress compression to achieve optimally small file size (attention: may cause small loss of precision; only for mzML data)" help=""/>
45 <expand macro="advanced_options"> 51 <param name="full_meta" argument="-full_meta" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Write full meta information into sqMass file (may require large amounts of memory)" help=""/>
46 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 52 <expand macro="adv_opts_macro">
53 <param name="lossy_mass_accuracy" argument="-lossy_mass_accuracy" type="float" optional="true" value="-1.0" label="Desired (absolute) m/z accuracy for lossy compression" help="(e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy)"/>
54 <param name="process_lowmemory" argument="-process_lowmemory" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to process the file on the fly without loading the whole file into memory first (only for conversions of mzXML/mzML to mzML)" help="Note: this flag will prevent conversion from spectra to chromatograms"/>
55 <param name="lowmem_batchsize" argument="-lowmem_batchsize" type="integer" optional="true" min="0" value="500" label="The batch size of the low memory conversion" help=""/>
56 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
57 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
58 <expand macro="list_string_san"/>
59 </param>
47 </expand> 60 </expand>
61 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
62 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
63 </param>
48 </inputs> 64 </inputs>
49 <outputs> 65 <outputs>
50 <data name="param_out" format="mzml"/> 66 <data name="out" label="${tool.name} on ${on_string}: out">
67 <change_format>
68 <when input="out_type" value="mzML" format="mzml"/>
69 <when input="out_type" value="sqMass" format="sqmass"/>
70 </change_format>
71 </data>
72 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
73 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
74 </data>
51 </outputs> 75 </outputs>
52 <help>This tool caches the spectra and chromatogram data of an mzML to disk. 76 <tests>
77 <expand macro="autotest_OpenSwathMzMLFileCacher"/>
78 <expand macro="manutest_OpenSwathMzMLFileCacher"/>
79 </tests>
80 <help><![CDATA[This tool caches the spectra and chromatogram data of an mzML to disk.
53 81
54 82
55 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_OpenSwathMzMLFileCacher.html</help> 83 For more information, visit http://www.openms.de/documentation/UTILS_OpenSwathMzMLFileCacher.html]]></help>
84 <expand macro="references"/>
56 </tool> 85 </tool>