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comparison tepid-discover.xml @ 5:afe2a09f802b draft default tip

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planemo upload for repository https://github.com/ListerLab/TEPID commit 48d24b91382cfbe7749d131657efbad47a28f569-dirty
author mvdbeek
date Fri, 06 Jan 2017 08:36:08 -0500
parents df634cd04be7
children
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4:df634cd04be7 5:afe2a09f802b
50 <param name="insertions" argument="--insertions" type="boolean" truevalue="--insertions" falsevalue="" label="Find insertions only?"/> 50 <param name="insertions" argument="--insertions" type="boolean" truevalue="--insertions" falsevalue="" label="Find insertions only?"/>
51 <param name="strict" argument="--strict" type="boolean" truevalue="--strict" falsevalue="" label="Report high-confidence variants only?"/> 51 <param name="strict" argument="--strict" type="boolean" truevalue="--strict" falsevalue="" label="Report high-confidence variants only?"/>
52 </inputs> 52 </inputs>
53 <outputs> 53 <outputs>
54 <data name="insertions_out" format="bed" label="tepid_discover insertions on ${on_string}"> 54 <data name="insertions_out" format="bed" label="tepid_discover insertions on ${on_string}">
55 <filter>not deletions</filter>
56 </data>
57 <data name="insertion_reads_out" format="txt" label="tepid_discover reads supporting insertions for ${on_string}">
58 <filter>not deletions</filter>
59 </data>
60 <data name="deletions_out" format="bed" label="tepid_discover deletions on ${on_string}">
55 <filter>not insertions</filter> 61 <filter>not insertions</filter>
56 </data> 62 </data>
57 <data name="insertion_reads_out" format="txt" label="tepid_discover reads supporting insertions for ${on_string}"> 63 <data name="deletion_reads_out" format="txt" label="tepid_discover reads supporting deletions for ${on_string}">
58 <filter>not insertions"</filter> 64 <filter>not insertions"</filter>
59 </data>
60 <data name="deletions_out" format="bed" label="tepid_discover deletions on ${on_string}">
61 <filter>not deletions</filter>
62 </data>
63 <data name="deletion_reads_out" format="txt" label="tepid_discover reads supporting deletions for ${on_string}">
64 <filter>not deletions</filter>
65 </data> 65 </data>
66 </outputs> 66 </outputs>
67 <tests> 67 <tests>
68 <test> 68 <test>
69 <param name="bowtie2_bam" value="conc.bam"/> 69 <param name="bowtie2_bam" value="conc.bam"/>
71 <param name="te_annotation_bed" value="TAIR9_TE.bed.gz" ftype="bed"/> 71 <param name="te_annotation_bed" value="TAIR9_TE.bed.gz" ftype="bed"/>
72 <output name="insertions_out" file="insertions_test.bed"/> 72 <output name="insertions_out" file="insertions_test.bed"/>
73 <output name="deletions_out" file="deletions_test.bed"/> 73 <output name="deletions_out" file="deletions_test.bed"/>
74 <output name="insertion_reads_out" file="insertion_reads_test.txt"/> 74 <output name="insertion_reads_out" file="insertion_reads_test.txt"/>
75 <output name="deletion_reads_out" file="deletion_reads_test.txt"/> 75 <output name="deletion_reads_out" file="deletion_reads_test.txt"/>
76 </test>
77 <test>
78 <param name="bowtie2_bam" value="conc.bam"/>
79 <param name="split_bam" value="split.bam"/>
80 <param name="te_annotation_bed" value="TAIR9_TE.bed.gz" ftype="bed"/>
81 <param name="deletions" value="true"/>
82 <output name="deletions_out" file="deletions_test.bed"/>
83 <output name="deletion_reads_out" file="deletion_reads_test.txt"/>
84 </test>
85 <test>
86 <param name="bowtie2_bam" value="conc.bam"/>
87 <param name="split_bam" value="split.bam"/>
88 <param name="te_annotation_bed" value="TAIR9_TE.bed.gz" ftype="bed"/>
89 <param name="insertions" value="true"/>
90 <output name="insertions_out" file="insertions_test.bed"/>
91 <output name="insertion_reads_out" file="insertion_reads_test.txt"/>
76 </test> 92 </test>
77 </tests> 93 </tests>
78 <help><![CDATA[ 94 <help><![CDATA[
79 TEPID -- transposable element polymorphism identification 95 TEPID -- transposable element polymorphism identification
80 96