Mercurial > repos > jjohnson > contig_annotation_tool

annotate cat_summarise.xml @ 3:18ece3d5bcde draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 3febcc9ba3d3717877c36bf96742209012a13ac4-dirty
author jjohnson
date Tue, 26 Nov 2019 15:42:14 -0500
parents ad7507073c3f
children 226949352e31
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
1 <tool id="cat_summarise" name="CAT summarise" version="@VERSION@.0">
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
2 <description>annotate with taxonomic classification</description>
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
3 <macros>
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
4 <import>macros.xml</import>
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
5 </macros>
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
6 <expand macro="requirements" />
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
7 <expand macro="version_command" />
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
9 CAT summarise -c '$contigs_fasta' -i '$input'
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
10 -o output_names_summary.txt
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
11 && @TXT2TSV@ -i output_names_summary.txt -o $output
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
12 ]]></command>
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
13 <inputs>
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
14 <param name="input" type="data" format="tabular" label="classification.official_names.txt"
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
15 help="The classication must be made with only_official names"/>
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
16 <param name="contigs_fasta" type="data" format="fasta" optional="true" label="contigs.fasta"
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
17 help="Required if a contig2classification.names"/>
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
18 </inputs>
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
19 <outputs>
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
20 <data name="output" format="tabular"/>
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
21 </outputs>
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
22 <tests>
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
23 <test>
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
24 <param name="input" ftype="tabular" value="test_contig.contig2classification.names.txt"/>
3
18ece3d5bcde planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 3febcc9ba3d3717877c36bf96742209012a13ac4-dirty
jjohnson
parents: 0
diff changeset
25 <param name="contigs_fasta" ftype="fasta" value="contigs.fasta"/>
0
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
26 <output name="output">
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
27 <assert_contents>
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
28 <has_text text="Firmicutes" />
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
29 </assert_contents>
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
30 </output>
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
31 </test>
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
32 </tests>
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
33 <help><![CDATA[
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
34 **CAT summarise**
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
35 Produce a summary report of assignments to the ofifcial taxonomic names.
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
36
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
37 @COMMON_HELP@
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
38 ]]></help>
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
39 <expand macro="citations" />
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
parents:
diff changeset
40 </tool>