Mercurial > repos > gga > apollo_export

comparison export.xml @ 10:c3b5bc8b4080 draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
author gga
date Mon, 02 Dec 2019 05:43:20 -0500
parents f45ad96c9e08
children b763acecfb57
comparison
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9:f45ad96c9e08 10:c3b5bc8b4080
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <code file="webapollo.py"/> 8 <code file="webapollo.py"/>
9 <command detect_errors="aggressive"><![CDATA[ 9 <command detect_errors="aggressive"><![CDATA[
10 python $__tool_directory__/export.py 10 @AUTH@
11 11 python '$__tool_directory__/export.py'
12 @ADMIN_AUTH@
13 12
14 @ORG_CN_OR_GUESS@ 13 @ORG_CN_OR_GUESS@
15 14
16 --gff "$gff_out" 15 --gff '$gff_out'
17 --fasta "$fasta_out" 16 --fasta_pep '$fasta_pep'
18 --json "$json_out" 17 --fasta_cds '$fasta_cds'
18 --fasta_cdna '$fasta_cdna'
19 --vcf '$vcf_out'
20 --json '$json_out'
19 21
20 "$__user_email__" 22 '$__user_email__'
21 23
22 ]]></command> 24 ]]></command>
23 <inputs> 25 <inputs>
24 <expand macro="cn_or_guess" /> 26 <expand macro="cn_or_guess" />
25 </inputs> 27 </inputs>
26 <outputs> 28 <outputs>
27 <data format="gff3" name="gff_out" label="Annotations from Apollo"/> 29 <data format="gff3" name="gff_out" label="Annotations from Apollo"/>
28 <data format="fasta" name="fasta_out" label="Sequence(s) from Apollo"/> 30 <data format="fasta" name="fasta_pep" label="Peptide sequences from Apollo"/>
31 <data format="fasta" name="fasta_cds" label="CDS sequences from Apollo"/>
32 <data format="fasta" name="fasta_cdna" label="cDNA sequences from Apollo"/>
33 <data format="vcf" name="vcf_out" label="Sequence alterations from Apollo"/>
29 <data format="json" name="json_out" label="Metadata from Apollo"> 34 <data format="json" name="json_out" label="Metadata from Apollo">
30 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" visible="true"/> 35 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" visible="true"/>
31 </data> 36 </data>
32 </outputs> 37 </outputs>
33 <tests> 38 <tests>
34 <test expect_failure="true"> 39 <test>
35 <conditional name="org_source"> 40 <conditional name="org_source">
36 <param name="source_select" value="direct"/> 41 <param name="source_select" value="direct"/>
37 <param name="org_raw" value="Test org" /> 42 <param name="org_raw" value="test_organism" />
38 </conditional> 43 </conditional>
39 <conditional name="cn_source"> 44 <conditional name="cn_source">
40 <param name="source_select" value="all"/> 45 <param name="source_select" value="all"/>
41 </conditional> 46 </conditional>
42 <expand macro="test_result" /> 47
48 <output name="gff_out">
49 <assert_contents>
50 <has_text text="##sequence-region Merlin 1 172788" />
51 <has_text text="owner=admin@local.host;" />
52 <has_text text="Name=cds-not-under-exon" />
53 </assert_contents>
54 </output>
55 <output name="fasta_pep" file="export/pep.fa" lines_diff="12"/>
56 <output name="fasta_cds" file="export/cds.fa" lines_diff="12"/>
57 <output name="fasta_cdna" file="export/cdna.fa" lines_diff="12"/>
58 <output name="vcf_out" file="export/out.vcf" lines_diff="4"/>
59 <output name="json_out">
60 <assert_contents>
61 <has_text text="test_organism" />
62 <has_text text="apollo_shared_dir/org1" />
63 </assert_contents>
64 </output>
43 </test> 65 </test>
44 </tests> 66 </tests>
45 <help><![CDATA[ 67 <help><![CDATA[
46 **What it does** 68 **What it does**
47 69