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comparison pepquery2_show_sets.xml @ 0:b9e1e95758e8 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
author galaxyp
date Sun, 06 Nov 2022 16:24:53 +0000
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children d39a43a076fc
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1 <tool id="pepquery2_show_sets" name="PepQuery2 Show Sets" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
2 <description>PepQueryDB datasets, Parameters, PTMs</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">pepquery</requirement>
8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[
10 echo "PepQuery2 Show Sets $sets"
11 #if 'PepQueryDB_datasets' in $sets
12 && pepquery -b show_full | sed 's/.*\(NO[.]\)/\1/' | grep '^[N1-9]' | sed 's/[ ][ ]*\$//' | sed 's/[ ][ ]*/\t/g' > '$pepquerydb'
13 #end if
14 #if 'parameter_sets' in $sets
15 && pepquery -p show | grep -v INFO | sed 's/^.\[m//' > $parameters
16 #end if
17 #if 'printPTM' in $sets
18 && pepquery -printPTM | grep -v INFO | sed 's/^.\[m//' > $ptm_list
19 #end if
20 ]]></command>
21 <inputs>
22 <param name="sets" type="select" multiple="true" optional="false" label="PepQuery Set">
23 <option value="PepQueryDB_datasets" selected="true">PepQueryDB Datasets</option>
24 <option value="parameter_sets">PepQuery Predefined Parameter Sets</option>
25 <option value="printPTM">PepQuery Modifications</option>
26 </param>
27 </inputs>
28 <outputs>
29 <data name="pepquerydb" format="tabular" label="PepQueryDB datasets">
30 <filter>'PepQueryDB_datasets' in sets</filter>
31 <actions>
32 <action name="comment_lines" type="metadata" default="1" />
33 <action name="column_names" type="metadata" default="NO.,dataset_name,short_name,parameter_set,species,data_type,n_spectra,n_ms_file,data_link" />
34 </actions>
35 </data>
36 <data name="parameters" format="txt" label="PepQuery Predefined Parameter Sets">
37 <filter>'parameter_sets' in sets</filter>
38 </data>
39 <data name="ptm_list" format="tabular" label="PepQuery Modifications">
40 <filter>'printPTM' in sets</filter>
41 <actions>
42 <action name="comment_lines" type="metadata" default="1" />
43 <action name="column_names" type="metadata" default="mod_id,mod_name,mod_mass,mod_type,mod_category,unimod_accession" />
44 </actions>
45 </data>
46 </outputs>
47 <tests>
48 <test>
49 <output name="pepquerydb">
50 <assert_contents>
51 <has_text text="CPTAC_PDA_Discovery_Study_Proteome_PDC000270" />
52 </assert_contents>
53 </output>
54 </test>
55 </tests>
56 <help><![CDATA[
57 **Show available: PepQueryDB Datasets, Parameter Sets, and PTMs** *(Post Translational Modifications)*
58
59 @PEPQUERY_DOCUMANTATION_URL@
60
61 **PepQueryDB Datasets**
62
63 - Shows a table of all the indexed MS/MS datasets available in PepQueryDB.
64 - *java -jar pepquery-2.0.2.jar -b show_full*
65 - These datasets can be used for the **-b** option in **PepQuery**.
66 - The parameter_set value can be used in the **-p** option in **PepQuery**.
67 - Columns: NO. dataset_name short_name parameter_set species data_type n_spectra n_ms_file data_link
68
69
70 **PepQuery Predefined Parameter Sets**
71
72 - Shows the predefined Parameter Set Names with the option settings
73 - *java -jar pepquery-2.0.2.jar -p show*
74 - The parameterset names can be used for the **-p** option in **PepQuery**.
75
76
77 **PepQuery Modifications**
78
79 - Shows a table of the PTMs available
80 - *java -jar pepquery-2.0.2.jar -printPTM*
81 - The mod_id numbers can be used in the **-fixMOD** and **-varMOD** options in **PepQuery**.
82 - Columns: mod_id mod_name mod_mass mod_type mod_category unimod_accession
83
84 ]]></help>
85 <expand macro="citations" />
86 </tool>