Mercurial > repos > iuc > varscan_somatic
comparison macros.xml @ 1:31a38ce7e8ae draft
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
| author | iuc |
|---|---|
| date | Sun, 15 Jul 2018 09:19:25 -0400 |
| parents | 72b8ce355fae |
| children | 2fe9ebb98aad |
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| 0:72b8ce355fae | 1:31a38ce7e8ae |
|---|---|
| 20 <xml name="citations"> | 20 <xml name="citations"> |
| 21 <citations> | 21 <citations> |
| 22 <citation type="doi">10.1101/gr.129684.111</citation> | 22 <citation type="doi">10.1101/gr.129684.111</citation> |
| 23 </citations> | 23 </citations> |
| 24 </xml> | 24 </xml> |
| 25 | |
| 26 <xml name="input_pileups"> | |
| 27 <conditional name="pileup"> | |
| 28 <param name="pileup_select" type="select" label="How do you want to provide your pileup files?" help=""> | |
| 29 <option value="separated">As separated normal and tumor files</option> | |
| 30 <option value="combined">Normal and Tumor combined in one file</option> | |
| 31 </param> | |
| 32 <when value="separated"> | |
| 33 <param name="normal_pileup" format="pileup" type="data" label="Samtools pileup dataset for Normal" help=""/> | |
| 34 <param name="tumor_pileup" format="pileup" type="data" label="Samtools pileup dataset for Tumor" help=""/> | |
| 35 </when> | |
| 36 <when value="combined"> | |
| 37 <param name="combined_pileup" format="pileup" type="data" label="Samtools pileup dataset which has combined Normal and Tumor samples" help=""/> | |
| 38 </when> | |
| 39 </conditional> | |
| 40 </xml> | |
| 41 | |
| 42 <token name="@INPUT_PILEUPS@"> | |
| 43 #if $pileup.pileup_select == 'separated' | |
| 44 '${pileup.normal_pileup}' | |
| 45 '${pileup.tumor_pileup}' | |
| 46 galaxy_out | |
| 47 #else: | |
| 48 '${pileup.combined_pileup}' | |
| 49 galaxy_out | |
| 50 --mpileup 1 | |
| 51 #end if | |
| 52 | |
| 53 </token> | |
| 25 | 54 |
| 26 <xml name="min_coverage"> | 55 <xml name="min_coverage"> |
| 27 <param argument="--min-coverage" name="min_coverage" type="integer" value="8" min="1" max="200" | 56 <param argument="--min-coverage" name="min_coverage" type="integer" value="8" min="1" max="200" |
| 28 label="Minimum read depth" help="Minimum depth at a position to make a call"/> | 57 label="Minimum read depth" help="Minimum depth at a position to make a call"/> |
| 29 </xml> | 58 </xml> |