Mercurial > repos > gga > apollo_delete_features

comparison delete_features.xml @ 10:df0e4eb2dfa5 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 05:44:41 -0500
parents 2adc3aa47d15
children 21a8cad7dfa5
comparison
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9:2adc3aa47d15 10:df0e4eb2dfa5
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 @AUTH@
11
10 #if str($ask_one) == "yes": 12 #if str($ask_one) == "yes":
11 ## Nope, still don't trust them to not be dumb (or malicious), so we backup first. 13 ## Nope, still don't trust them to not be dumb (or malicious), so we backup first.
12 python $__tool_directory__/export.py 14 python '$__tool_directory__/export.py'
13 @ADMIN_AUTH@
14 @ORG_OR_GUESS@ 15 @ORG_OR_GUESS@
15 --gff "$gff_out" 16 --gff '$gff_out'
16 --fasta "$fasta_out" 17 --fasta_pep '$fasta_pep'
17 --json "$json_out" 18 --fasta_cds '$fasta_cds'
18 "$__user_email__" 19 --fasta_cdna '$fasta_cdna'
20 --vcf '$vcf_out'
21 --json '$json_out'
22 '$__user_email__'
19 23
20 && 24 &&
21 25
22 ## Now we delete 26 ## Now we delete
23 python $__tool_directory__/delete_features.py 27 python '$__tool_directory__/delete_features.py'
24 @ADMIN_AUTH@
25 @ORG_OR_GUESS@ 28 @ORG_OR_GUESS@
26 "$__user_email__" 29 '$__user_email__'
27 #if str($filter) != "all" 30 #if str($filter) != "all"
28 --type $filter 31 --type $filter
29 #end if 32 #end if
30 > $output; 33 > '$output';
31 #else 34 #else
32 echo "Nothing to do" > $output; 35 echo "Nothing to do" > '$output';
33 #end if 36 #end if
34 ]]></command> 37 ]]></command>
35 <inputs> 38 <inputs>
36 <expand macro="org_or_guess" /> 39 <expand macro="org_or_guess" />
37 <param name="filter" type="select" label="Feature Type Filter"> 40 <param name="filter" type="select" label="Feature Type Filter">
41 <option value="tRNA">tRNAs</option> 44 <option value="tRNA">tRNAs</option>
42 </param> 45 </param>
43 <param name="ask_one" type="boolean" truevalue="yes" falsevalue="" label="Are you SURE you want to do this?" help="It will PERMANENTLY delete all of the features on this organism."/> 46 <param name="ask_one" type="boolean" truevalue="yes" falsevalue="" label="Are you SURE you want to do this?" help="It will PERMANENTLY delete all of the features on this organism."/>
44 </inputs> 47 </inputs>
45 <outputs> 48 <outputs>
46 <data format="tabular" name="output" label="Process and Error Log"> 49 <data format="txt" name="output" label="Process and Error Log">
47 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" visible="true"/> 50 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" visible="true"/>
48 </data> 51 </data>
49 52
50 <data format="gff3" name="gff_out" label="Annotations from Apollo" hidden="true"/> 53 <data format="gff3" name="gff_out" label="Annotations from Apollo"/>
51 <data format="fasta" name="fasta_out" label="Sequence(s) from Apollo" hidden="true"/> 54 <data format="fasta" name="fasta_pep" label="Peptide sequences from Apollo"/>
52 <data format="json" name="json_out" label="Metadata from Apollo" hidden="true"/> 55 <data format="fasta" name="fasta_cds" label="CDS sequences from Apollo"/>
56 <data format="fasta" name="fasta_cdna" label="cDNA sequences from Apollo"/>
57 <data format="vcf" name="vcf_out" label="Sequence alterations from Apollo"/>
58 <data format="json" name="json_out" label="Metadata from Apollo"/>
53 </outputs> 59 </outputs>
54 <tests> 60 <tests>
55 <test expect_failure="true"> 61 <test>
56 <conditional name="org_source"> 62 <conditional name="org_source">
57 <param name="source_select" value="direct"/> 63 <param name="source_select" value="direct"/>
58 <param name="org_raw" value="Test org" /> 64 <param name="org_raw" value="org4" />
59 </conditional> 65 </conditional>
60 <param name="filter" value="all"/> 66 <param name="filter" value="all"/>
61 <param name="ask_one" value="yes"/> 67 <param name="ask_one" value="yes"/>
62 <expand macro="test_result" /> 68
69 <output name="gff_out">
70 <assert_contents>
71 <has_text text="##sequence-region Merlin 1 172788" />
72 <has_text text="owner=admin@local.host;" />
73 <has_text text="Name=cds-not-under-exon" />
74 </assert_contents>
75 </output>
76 <output name="fasta_pep" file="export/pep.fa" lines_diff="12"/>
77 <output name="fasta_cds" file="export/cds.fa" lines_diff="12"/>
78 <output name="fasta_cdna" file="export/cdna.fa" lines_diff="12"/>
79 <output name="vcf_out" file="export/out.vcf" lines_diff="4"/>
80 <output name="json_out">
81 <assert_contents>
82 <has_text text="org4" />
83 <has_text text="apollo_shared_dir/org4" />
84 </assert_contents>
85 </output>
86 <output name="output">
87 <assert_contents>
88 <has_text text="Deleted" />
89 <has_text text="[type=mRNA]" />
90 </assert_contents>
91 </output>
63 </test> 92 </test>
64 </tests> 93 </tests>
65 <help><![CDATA[ 94 <help><![CDATA[
66 **What it does** 95 **What it does**
67 96