Mercurial > repos > galaxyp > openms_idsplitter
comparison IDSplitter.xml @ 9:629b818f162c draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author | galaxyp |
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date | Wed, 09 Sep 2020 12:44:13 +0000 |
parents | 0a61c5337abf |
children | de2d6f629cea |
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8:b2f56dbfd906 | 9:629b818f162c |
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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="IDSplitter" name="IDSplitter" version="2.3.0"> | 4 <tool id="IDSplitter" name="IDSplitter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> |
5 <description>Splits protein/peptide identifications off of annotated data files</description> | 5 <description>Splits protein/peptide identifications off of annotated data files</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">IDSplitter</token> | 7 <token name="@EXECUTABLE@">IDSplitter</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[IDSplitter | 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($in.ext)' && | |
21 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
22 mkdir out && | |
17 #end if | 23 #end if |
18 #if $param_out: | 24 #if "id_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
19 -out $param_out | 25 mkdir id_out && |
20 #end if | 26 #end if |
21 #if $param_id_out: | 27 |
22 -id_out $param_id_out | 28 ## Main program call |
29 | |
30 set -o pipefail && | |
31 @EXECUTABLE@ -write_ctd ./ && | |
32 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && | |
33 @EXECUTABLE@ -ini @EXECUTABLE@.ctd | |
34 -in | |
35 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' | |
36 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
37 -out | |
38 'out/output.${in.ext}' | |
23 #end if | 39 #end if |
24 #if $adv_opts.adv_opts_selector=='advanced': | 40 #if "id_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') |
25 #if $adv_opts.param_force: | 41 -id_out |
26 -force | 42 'id_out/output.${gxy2omsext("idxml")}' |
27 #end if | 43 #end if |
44 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 | |
45 | tee '$stdout' | |
28 #end if | 46 #end if |
29 ]]></command> | 47 |
48 ## Postprocessing | |
49 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
50 && mv 'out/output.${in.ext}' '$out' | |
51 #end if | |
52 #if "id_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') | |
53 && mv 'id_out/output.${gxy2omsext("idxml")}' '$id_out' | |
54 #end if | |
55 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS | |
56 && mv '@EXECUTABLE@.ctd' '$ctd_out' | |
57 #end if]]></command> | |
58 <configfiles> | |
59 <inputs name="args_json" data_style="paths"/> | |
60 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> | |
61 </configfiles> | |
30 <inputs> | 62 <inputs> |
31 <param name="param_in" type="data" format="mzml,featurexml,consensusxml" optional="False" label="Input file (data annotated with identifications)" help="(-in) "/> | 63 <param name="in" argument="-in" type="data" format="consensusxml,featurexml,mzml" optional="false" label="Input file (data annotated with identifications)" help=" select consensusxml,featurexml,mzml data sets(s)"/> |
32 <expand macro="advanced_options"> | 64 <expand macro="adv_opts_macro"> |
33 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | 65 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> |
66 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | |
67 <expand macro="list_string_san"/> | |
68 </param> | |
34 </expand> | 69 </expand> |
70 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false"> | |
71 <option value="out_FLAG">out (Enables the test mode (needed for internal use only))</option> | |
72 <option value="id_out_FLAG">id_out (Enables the test mode (needed for internal use only))</option> | |
73 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | |
74 </param> | |
35 </inputs> | 75 </inputs> |
36 <outputs> | 76 <outputs> |
37 <data name="param_out" metadata_source="param_in" format="input"/> | 77 <data name="out" label="${tool.name} on ${on_string}: out" format_source="in" metadata_source="in"> |
38 <data name="param_id_out" format="idxml"/> | 78 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter> |
79 </data> | |
80 <data name="id_out" label="${tool.name} on ${on_string}: id_out" format="idxml"> | |
81 <filter>OPTIONAL_OUTPUTS is not None and "id_out_FLAG" in OPTIONAL_OUTPUTS</filter> | |
82 </data> | |
83 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout"> | |
84 <filter>OPTIONAL_OUTPUTS is None</filter> | |
85 </data> | |
86 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | |
87 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | |
88 </data> | |
39 </outputs> | 89 </outputs> |
40 <help>Splits protein/peptide identifications off of annotated data files | 90 <tests> |
91 <expand macro="autotest_IDSplitter"/> | |
92 <expand macro="manutest_IDSplitter"/> | |
93 </tests> | |
94 <help><![CDATA[Splits protein/peptide identifications off of annotated data files | |
41 | 95 |
42 | 96 |
43 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_IDSplitter.html</help> | 97 For more information, visit http://www.openms.de/documentation/UTILS_IDSplitter.html]]></help> |
98 <expand macro="references"/> | |
44 </tool> | 99 </tool> |