Mercurial > repos > greg > create_genome_tracks
comparison create_genome_tracks.xml @ 0:27d5a1d744fd draft
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| author | greg |
|---|---|
| date | Fri, 10 Nov 2017 13:19:37 -0500 |
| parents | |
| children | a0766c75ef2f |
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| -1:000000000000 | 0:27d5a1d744fd |
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| 1 <tool id="create_genome_tracks" name="Create genome tracks" version="1.0.0"> | |
| 2 <description>from IDEAS statistics</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="2.4.27">bedops</requirement> | |
| 5 <requirement type="package" version="1.4.4">r-optparse</requirement> | |
| 6 <requirement type="package" version="332">ucsc-bedtobigbed</requirement> | |
| 7 </requirements> | |
| 8 <command detect_errors="exit_code"><![CDATA[ | |
| 9 Rscript '$__tool_directory__/create_genome_tracks.R' | |
| 10 -b $parameter_file.metadata.dbkey | |
| 11 -c '$chromInfo' | |
| 12 -h test | |
| 13 -p '$parameter_file' | |
| 14 -s '$state_file' | |
| 15 -t 'http://bx.psu.edu/~yuzhang/tmp/' | |
| 16 -u '$output_track_db' | |
| 17 -v '$output_build' | |
| 18 -w '$output_hub']]></command> | |
| 19 <inputs> | |
| 20 <param name="state_file" type="data" format="txt" label="IDEAS epigenetic states and position classes dataset"> | |
| 21 <validator type="empty_field"/> | |
| 22 <validator type="unspecified_build"/> | |
| 23 </param> | |
| 24 <param name="parameter_file" type="data" format="tabular" label="IDEAS epigenetic state frequency, mean and variance parameters dataset"> | |
| 25 <validator type="empty_field"/> | |
| 26 <validator type="unspecified_build"/> | |
| 27 </param> | |
| 28 </inputs> | |
| 29 <outputs> | |
| 30 <data name="output_track_db" format="bigbed" label="${tool.name} (track db) on ${on_string}"/> | |
| 31 <data name="output_build" format="txt" label="${tool.name} (genome build) on ${on_string}"/> | |
| 32 <data name="output_hub" format="txt" label="${tool.name} (hub) on ${on_string}"/> | |
| 33 </outputs> | |
| 34 <tests> | |
| 35 <test> | |
| 36 </test> | |
| 37 </tests> | |
| 38 <help> | |
| 39 **What it does** | |
| 40 | |
| 41 ----- | |
| 42 | |
| 43 **Required options** | |
| 44 | |
| 45 </help> | |
| 46 <citations> | |
| 47 <citation type="doi">10.1093/nar/gkw278</citation> | |
| 48 </citations> | |
| 49 </tool> |