Mercurial > repos > gga > apollo_delete_organism

comparison delete_organism.xml @ 10:dd63c6e11a95 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 05:48:12 -0500
parents 1575f11ac6fc
children 6ea838bf1f2f
comparison
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9:1575f11ac6fc 10:dd63c6e11a95
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 #if str($ask_two) == "yes": 13 #if str($ask_two) == "yes":
12 ## Nope, still don't trust them to not be dumb (or malicious), so we backup first. 14 ## Nope, still don't trust them to not be dumb (or malicious), so we backup first.
13 python $__tool_directory__/export.py 15 python '$__tool_directory__/export.py'
14 @ADMIN_AUTH@
15 @ORG_OR_GUESS@ 16 @ORG_OR_GUESS@
16 --gff "$gff_out" 17 --gff '$gff_out'
17 --fasta "$fasta_out" 18 --fasta_pep '$fasta_pep'
18 --json "$json_out" 19 --fasta_cds '$fasta_cds'
19 "$__user_email__" 20 --fasta_cdna '$fasta_cdna'
21 --vcf '$vcf_out'
22 --json '$json_out'
23 '$__user_email__'
20 24
21 && 25 &&
22 26
23 ## Now we delete 27 ## Now we delete
24 python $__tool_directory__/delete_organism.py 28 python '$__tool_directory__/delete_organism.py'
25 @ADMIN_AUTH@
26 @ORG_OR_GUESS@ 29 @ORG_OR_GUESS@
27 "$__user_email__" 30 '$__user_email__'
28 > $output; 31 >> '$output';
29 #else 32 #else
30 echo "Nothing to do" > $output; 33 echo "Nothing to do" > '$output';
31 #end if 34 #end if
32 #else 35 #else
33 echo "Nothing to do" > $output; 36 echo "Nothing to do" > '$output';
34 #end if 37 #end if
35 ]]></command> 38 ]]></command>
36 <inputs> 39 <inputs>
37 <expand macro="org_or_guess" /> 40 <expand macro="org_or_guess" />
38 <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."/> 41 <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."/>
39 <param name="ask_two" type="boolean" truevalue="yes" falsevalue="" label="Are you really, really SURE you want to do this?" help="There's NO coming back from this."/> 42 <param name="ask_two" type="boolean" truevalue="yes" falsevalue="" label="Are you really, really SURE you want to do this?" help="There's NO coming back from this."/>
40 </inputs> 43 </inputs>
41 <outputs> 44 <outputs>
42 <data format="tabular" name="output" label="Process and Error Log"> 45 <data format="json" name="output" label="Process and Error Log">
43 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" visible="true"/> 46 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" visible="true"/>
44 </data> 47 </data>
45 48
46 <data format="gff3" name="gff_out" label="Annotations from Apollo" hidden="true"/> 49 <data format="gff3" name="gff_out" label="Annotations from Apollo"/>
47 <data format="fasta" name="fasta_out" label="Sequence(s) from Apollo" hidden="true"/> 50 <data format="fasta" name="fasta_pep" label="Peptide sequences from Apollo"/>
48 <data format="json" name="json_out" label="Metadata from Apollo" hidden="true"/> 51 <data format="fasta" name="fasta_cds" label="CDS sequences from Apollo"/>
52 <data format="fasta" name="fasta_cdna" label="cDNA sequences from Apollo"/>
53 <data format="vcf" name="vcf_out" label="Sequence alterations from Apollo"/>
54 <data format="json" name="json_out" label="Metadata from Apollo"/>
49 </outputs> 55 </outputs>
50 <tests> 56 <tests>
51 <test expect_failure="true"> 57 <test>
52 <conditional name="org_source"> 58 <conditional name="org_source">
53 <param name="source_select" value="direct"/> 59 <param name="source_select" value="direct"/>
54 <param name="org_raw" value="Test org" /> 60 <param name="org_raw" value="org3" />
55 </conditional> 61 </conditional>
56 <param name="filter" value="all"/> 62 <param name="ask_one" value="true"/>
57 <param name="ask_one" value="yes"/> 63 <param name="ask_two" value="true"/>
58 <param name="ask_two" value="yes"/> 64
59 <expand macro="test_result" /> 65 <output name="gff_out">
66 <assert_contents>
67 <has_text text="##sequence-region Merlin 1 172788" />
68 <has_text text="owner=admin@local.host;" />
69 <has_text text="Name=cds-not-under-exon" />
70 </assert_contents>
71 </output>
72 <output name="fasta_pep" file="export/pep.fa" lines_diff="12"/>
73 <output name="fasta_cds" file="export/cds.fa" lines_diff="12"/>
74 <output name="fasta_cdna" file="export/cdna.fa" lines_diff="12"/>
75 <output name="vcf_out" file="export/out.vcf" lines_diff="4"/>
76 <output name="json_out">
77 <assert_contents>
78 <has_text text="org3" />
79 <has_text text="Foo3" />
80 </assert_contents>
81 </output>
82 <output name="output">
83 <assert_contents>
84 <has_text text="org3" />
85 <has_text text="Foo3" />
86 </assert_contents>
87 </output>
60 </test> 88 </test>
61 </tests> 89 </tests>
62 <help><![CDATA[ 90 <help><![CDATA[
63 **What it does** 91 **What it does**
64 92