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comparison tools/blastxml_to_top_descr/blastxml_to_top_descr.xml @ 13:8dc4ba7eba5d draft default tip

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v0.1.2 with Python 3.9 declaration
author peterjc
date Sun, 17 Sep 2023 13:01:56 +0000
parents fe1ed74793c9
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12:fe1ed74793c9 13:8dc4ba7eba5d
1 <tool id="blastxml_to_top_descr" name="BLAST top hit descriptions" version="0.1.1"> 1 <tool id="blastxml_to_top_descr" name="BLAST top hit descriptions" version="0.1.2" profile="16.10">
2 <description>Make a table from BLAST output</description> 2 <description>Make a table from BLAST output</description>
3 <version_command interpreter="python">blastxml_to_top_descr.py --version</version_command> 3 <requirements>
4 <command interpreter="python"> 4 <requirement type="package" version="3.9">python</requirement>
5 blastxml_to_top_descr.py 5 </requirements>
6 -f "$input.in_format" 6 <version_command>
7 python $__tool_directory__/blastxml_to_top_descr.py --version
8 </version_command>
9 <command detect_errors="aggressive">
10 python $__tool_directory__/blastxml_to_top_descr.py
11 -f '$input.in_format'
7 #if $input.in_format == "tabular": 12 #if $input.in_format == "tabular":
8 --qseqid $input.qseqid 13 --qseqid $input.qseqid
9 --sseqid $input.sseqid 14 --sseqid $input.sseqid
10 --salltitles $input.salltitles 15 --salltitles $input.salltitles
11 #end if 16 #end if
12 -o "${tabular_file}" 17 -o '${tabular_file}'
13 -t ${topN} 18 -t ${topN}
14 "${in_file}" 19 '${in_file}'
15 </command> 20 </command>
16 <stdio>
17 <!-- Assume anything other than zero is an error -->
18 <exit_code range="1:" />
19 <exit_code range=":-1" />
20 </stdio>
21 <inputs> 21 <inputs>
22 <conditional name="input"> 22 <conditional name="input">
23 <param name="in_format" type="select" label="Input format"> 23 <param name="in_format" type="select" label="Input format">
24 <option value="blastxml" select="True">BLAST XML</option> 24 <option value="blastxml" selected="true">BLAST XML</option>
25 <option value="tabular">Tabular</option> 25 <option value="tabular">Tabular</option>
26 </param> 26 </param>
27 <when value="blastxml"> 27 <when value="blastxml">
28 <param name="in_file" type="data" format="blastxml" label="BLAST results as XML"/> 28 <param name="in_file" type="data" format="blastxml" label="BLAST results as XML"/>
29 </when> 29 </when>
30 <when value="tabular"> 30 <when value="tabular">
31 <param name="in_file" type="data" format="tabular" label="BLAST results as tabular"/> 31 <param name="in_file" type="data" format="tabular" label="BLAST results as tabular"/>
32 <param name="qseqid" type="data_column" data_ref="in_file" 32 <param name="qseqid" type="data_column" data_ref="in_file"
33 multiple="False" numerical="False" default_value="1" value="1" 33 multiple="false" numerical="false" default_value="1" value="1"
34 label="Column containing query ID (qseqid)" 34 label="Column containing query ID (qseqid)"
35 help="This is column 1 in standard BLAST tabular output" /> 35 help="This is column 1 in standard BLAST tabular output" />
36 <param name="sseqid" type="data_column" data_ref="in_file" 36 <param name="sseqid" type="data_column" data_ref="in_file"
37 multiple="False" numerical="False" default_value="2" value="2" 37 multiple="false" numerical="false" default_value="2" value="2"
38 label="Column containing match ID (sseqid)" 38 label="Column containing match ID (sseqid)"
39 help="This is column 2 in standard BLAST tabular output"/> 39 help="This is column 2 in standard BLAST tabular output"/>
40 <param name="salltitles" type="data_column" data_ref="in_file" 40 <param name="salltitles" type="data_column" data_ref="in_file"
41 multiple="False" numerical="False" default_value="25" value="25" 41 multiple="false" numerical="false" default_value="25" value="25"
42 label="Column containing containing descriptions (salltitles)" 42 label="Column containing containing descriptions (salltitles)"
43 help="This is column 25 in the default extended BLAST tabular output"/> 43 help="This is column 25 in the default extended BLAST tabular output"/>
44 </when> 44 </when>
45 </conditional> 45 </conditional>
46 <param name="topN" type="integer" min="1" max="100" optional="false" label="Number of descriptions" value="3"/> 46 <param name="topN" type="integer" min="1" max="100" optional="false" label="Number of descriptions" value="3"/>
47 </inputs> 47 </inputs>
48 <outputs> 48 <outputs>
49 <data name="tabular_file" format="tabular" label="Top $topN descriptions from $input.in_file.name" /> 49 <data name="tabular_file" format="tabular" label="Top $topN descriptions from $input.in_file.name" />
50 </outputs> 50 </outputs>
51 <requirements>
52 </requirements>
53 <tests> 51 <tests>
54 <test> 52 <test>
55 <param name="in_format" value="blastxml" /> 53 <param name="in_format" value="blastxml" />
56 <param name="in_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" /> 54 <param name="in_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" />
57 <param name="topN" value="3" /> 55 <param name="topN" value="3" />
100 cite: 98 cite:
101 99
102 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). 100 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
103 Galaxy tools and workflows for sequence analysis with applications 101 Galaxy tools and workflows for sequence analysis with applications
104 in molecular plant pathology. PeerJ 1:e167 102 in molecular plant pathology. PeerJ 1:e167
105 http://dx.doi.org/10.7717/peerj.167 103 https://doi.org/10.7717/peerj.167
106 104
107 This wrapper is available to install into other Galaxy Instances via the Galaxy 105 This wrapper is available to install into other Galaxy Instances via the Galaxy
108 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr 106 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
109 107
110 </help> 108 </help>