Mercurial > repos > mvdbeek > bam_readtagger
comparison extract_variants.xml @ 70:f383ca1c5033 draft
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
| author | mvdbeek |
|---|---|
| date | Tue, 05 Nov 2019 05:06:18 -0500 |
| parents | 97411db5f752 |
| children | b090e190c813 |
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| 69:97411db5f752 | 70:f383ca1c5033 |
|---|---|
| 1 <tool id="extract_variants" name="Extract variant fragments" version="0.5.16"> | 1 <tool id="extract_variants" name="Extract variant fragments" version="0.5.17"> |
| 2 <description>from long reads</description> | 2 <description>from long reads</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="0.5.16">readtagger</requirement> | 4 <requirement type="package" version="0.5.17">readtagger</requirement> |
| 5 </requirements> | 5 </requirements> |
| 6 <version_command>extract_variants --version</version_command> | 6 <version_command>extract_variants --version</version_command> |
| 7 <command detect_errors="aggressive"><![CDATA[ | 7 <command detect_errors="aggressive"><![CDATA[ |
| 8 ln -fs '$insert_reference.fields.path' reference.fa && | 8 ln -fs '$insert_reference.fields.path' reference.fa && |
| 9 extract_variants '$input' '$output' reference.fa | 9 extract_variants '$input' '$output_alignment' reference.fa && |
| 10 summarize_fragments '$output_alignment' '$output_tabular' | |
| 10 ]]></command> | 11 ]]></command> |
| 11 <inputs> | 12 <inputs> |
| 12 <param name="input" label="Select alignment for which to extract variants" type="data" format="bam,cram"/> | 13 <param name="input" label="Select alignment for which to extract variants" type="data" format="bam,cram"/> |
| 13 <param name="insert_reference" label="Select a reference. If a variant aligns against this reference it will be retained" type="select"> | 14 <param name="insert_reference" label="Select a reference. If a variant aligns against this reference it will be retained" type="select"> |
| 14 <options from_data_table="all_fasta"/> | 15 <options from_data_table="all_fasta"/> |
| 15 </param> | 16 </param> |
| 16 </inputs> | 17 </inputs> |
| 17 <outputs> | 18 <outputs> |
| 18 <data name="output" format_source="input"/> | 19 <data name="output_alignment" format_source="input" label="${tool.name} on ${on_string}: alignment"/> |
| 20 <data name="output_tabular" format="tabular" label="${tool.name} on ${on_string}: summary"/> | |
| 19 </outputs> | 21 </outputs> |
| 20 <tests> | 22 <tests> |
| 21 <test> | 23 <test> |
| 22 <param name="input" value="long_insertion.bam" ftype="bam"/> | 24 <param name="input" value="long_insertion.bam" ftype="bam"/> |
| 23 <param name="insert_reference" value="transposon"/> | 25 <param name="insert_reference" value="transposon"/> |
| 24 <output name="output" file="long_insert_tagged.bam" ftype="bam"/> | 26 <output name="output_alignment" file="long_insert_tagged.bam" ftype="bam"/> |
| 27 <output name="output_tabular" file="long_insert_tagged.tab" ftype="tabular"/> | |
| 25 </test> | 28 </test> |
| 26 </tests> | 29 </tests> |
| 27 <help><![CDATA[ | 30 <help><![CDATA[ |
| 28 | 31 |
| 29 Extract variants will find soft-clipped alignments and alignments with insertions, | 32 Extract variants will find soft-clipped alignments and alignments with insertions, |