Mercurial > repos > galaxyp > openms_qcembedder
comparison QCEmbedder.xml @ 9:254e748f243a 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 12:47:21 +0000 |
parents | 059c20a50b1d |
children | 2c6f5858e89a |
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8:0d3ee005b033 | 9:254e748f243a |
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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="QCEmbedder" name="QCEmbedder" version="2.3.0"> | 4 <tool id="QCEmbedder" name="QCEmbedder" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> |
5 <description>Attaches a table or an image to a given qc parameter.</description> | 5 <description>Attaches a table or an image to a given qc parameter.</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">QCEmbedder</token> | 7 <token name="@EXECUTABLE@">QCEmbedder</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[QCEmbedder | 15 @EXT_FOO@ |
16 #import re | |
14 | 17 |
15 #if $param_in: | 18 ## Preprocessing |
16 -in $param_in | 19 #if $in: |
20 mkdir in && | |
21 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && | |
17 #end if | 22 #end if |
18 #if $param_qp_att_acc: | 23 #if $run: |
19 -qp_att_acc "$param_qp_att_acc" | 24 mkdir run && |
25 ln -s '$run' 'run/${re.sub("[^\w\-_]", "_", $run.element_identifier)}.$gxy2omsext($run.ext)' && | |
20 #end if | 26 #end if |
21 #if $param_cv_acc: | 27 #if $plot: |
22 -cv_acc "$param_cv_acc" | 28 mkdir plot && |
29 ln -s '$plot' 'plot/${re.sub("[^\w\-_]", "_", $plot.element_identifier)}.$gxy2omsext($plot.ext)' && | |
23 #end if | 30 #end if |
24 #if $param_run: | 31 #if $table: |
25 -run $param_run | 32 mkdir table && |
33 ln -s '$table' 'table/${re.sub("[^\w\-_]", "_", $table.element_identifier)}.$gxy2omsext($table.ext)' && | |
26 #end if | 34 #end if |
27 #if $param_name: | 35 mkdir out && |
28 -name "$param_name" | 36 |
37 ## Main program call | |
38 | |
39 set -o pipefail && | |
40 @EXECUTABLE@ -write_ctd ./ && | |
41 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && | |
42 @EXECUTABLE@ -ini @EXECUTABLE@.ctd | |
43 #if $in: | |
44 -in | |
45 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' | |
29 #end if | 46 #end if |
30 #if $param_plot: | 47 #if $run: |
31 -plot $param_plot | 48 -run |
49 'run/${re.sub("[^\w\-_]", "_", $run.element_identifier)}.$gxy2omsext($run.ext)' | |
32 #end if | 50 #end if |
33 #if $param_table: | 51 #if $plot: |
34 -table $param_table | 52 -plot |
53 'plot/${re.sub("[^\w\-_]", "_", $plot.element_identifier)}.$gxy2omsext($plot.ext)' | |
35 #end if | 54 #end if |
36 #if $param_out: | 55 #if $table: |
37 -out $param_out | 56 -table |
57 'table/${re.sub("[^\w\-_]", "_", $table.element_identifier)}.$gxy2omsext($table.ext)' | |
38 #end if | 58 #end if |
39 #if $adv_opts.adv_opts_selector=='advanced': | 59 -out |
40 #if $adv_opts.param_force: | 60 'out/output.${gxy2omsext("qcml")}' |
41 -force | 61 |
42 #end if | 62 ## Postprocessing |
43 #end if | 63 && mv 'out/output.${gxy2omsext("qcml")}' '$out' |
44 ]]></command> | 64 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS |
65 && mv '@EXECUTABLE@.ctd' '$ctd_out' | |
66 #end if]]></command> | |
67 <configfiles> | |
68 <inputs name="args_json" data_style="paths"/> | |
69 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> | |
70 </configfiles> | |
45 <inputs> | 71 <inputs> |
46 <param name="param_in" type="data" format="qcml" optional="True" label="Input qcml file" help="(-in) "/> | 72 <param name="in" argument="-in" type="data" format="qcml" optional="true" label="Input qcml file" help=" select qcml data sets(s)"/> |
47 <param name="param_qp_att_acc" type="text" size="30" label="Defines the qp cv accession of the qp to which the table/image is attached" help="(-qp_att_acc) "> | 73 <param name="qp_att_acc" argument="-qp_att_acc" type="text" optional="true" value="" label="Defines the qp cv accession of the qp to which the table/image is attached" help=""> |
48 <sanitizer> | 74 <expand macro="list_string_san"/> |
49 <valid initial="string.printable"> | |
50 <remove value="'"/> | |
51 <remove value="""/> | |
52 </valid> | |
53 </sanitizer> | |
54 </param> | 75 </param> |
55 <param name="param_cv_acc" type="text" size="30" label="Defines the cv accession of the attachment" help="(-cv_acc) "> | 76 <param name="cv_acc" argument="-cv_acc" type="text" optional="false" value="" label="Defines the cv accession of the attachment" help=""> |
56 <sanitizer> | 77 <expand macro="list_string_san"/> |
57 <valid initial="string.printable"> | |
58 <remove value="'"/> | |
59 <remove value="""/> | |
60 </valid> | |
61 </sanitizer> | |
62 </param> | 78 </param> |
63 <param name="param_run" type="data" format="mzml" optional="True" label="The file that defined the run under which the qp for the attachment is aggregated as mzML file" help="(-run) The file is only used to extract the run name from the file name"/> | 79 <param name="run" argument="-run" type="data" format="mzml" optional="true" label="The file that defined the run under which the qp for the attachment is aggregated as mzML file" help="The file is only used to extract the run name from the file name select mzml data sets(s)"/> |
64 <param name="param_name" type="text" size="30" label="If no file for the run was given (or if the target qp is contained in a set), at least a name of the target run/set containing the the qp for the attachment has to be given" help="(-name) "> | 80 <param name="name" argument="-name" type="text" optional="true" value="" label="If no file for the run was given (or if the target qp is contained in a set), at least a name of the target run/set containing the the qp for the attachment has to be given" help=""> |
65 <sanitizer> | 81 <expand macro="list_string_san"/> |
66 <valid initial="string.printable"> | |
67 <remove value="'"/> | |
68 <remove value="""/> | |
69 </valid> | |
70 </sanitizer> | |
71 </param> | 82 </param> |
72 <param name="param_plot" type="data" format="PNG" optional="True" label="If a plot image is to be attached to a qp, this has to be specified here" help="(-plot) "/> | 83 <param name="plot" argument="-plot" type="data" format="png" optional="true" label="If a plot image is to be attached to a qp, this has to be specified here" help=" select png data sets(s)"/> |
73 <param name="param_table" type="data" format="tabular" optional="True" label="If a table is to be attached to a qp, this has to be specified here" help="(-table) "/> | 84 <param name="table" argument="-table" type="data" format="csv" optional="true" label="If a table is to be attached to a qp, this has to be specified here" help=" select csv data sets(s)"/> |
74 <expand macro="advanced_options"> | 85 <expand macro="adv_opts_macro"> |
75 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | 86 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> |
87 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | |
88 <expand macro="list_string_san"/> | |
89 </param> | |
76 </expand> | 90 </expand> |
91 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> | |
92 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | |
93 </param> | |
77 </inputs> | 94 </inputs> |
78 <outputs> | 95 <outputs> |
79 <data name="param_out" format="qcml"/> | 96 <data name="out" label="${tool.name} on ${on_string}: out" format="qcml"/> |
97 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | |
98 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | |
99 </data> | |
80 </outputs> | 100 </outputs> |
81 <help>Attaches a table or an image to a given qc parameter. | 101 <tests> |
102 <expand macro="autotest_QCEmbedder"/> | |
103 <expand macro="manutest_QCEmbedder"/> | |
104 </tests> | |
105 <help><![CDATA[Attaches a table or an image to a given qc parameter. | |
82 | 106 |
83 | 107 |
84 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_QCEmbedder.html</help> | 108 For more information, visit http://www.openms.de/documentation/UTILS_QCEmbedder.html]]></help> |
109 <expand macro="references"/> | |
85 </tool> | 110 </tool> |