Mercurial > repos > dpryan79 > bwameth
comparison bwameth.xml @ 18:352e0213806c draft
Uploaded
| author | dpryan79 |
|---|---|
| date | Wed, 14 Sep 2016 07:53:18 -0400 |
| parents | b55c12d26066 |
| children | 5924e53ef39c |
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| 17:b55c12d26066 | 18:352e0213806c |
|---|---|
| 36 #if $single_or_paired.single_or_paired_opts == 'single': | 36 #if $single_or_paired.single_or_paired_opts == 'single': |
| 37 $single_or_paired.input_singles | 37 $single_or_paired.input_singles |
| 38 #else: | 38 #else: |
| 39 $single_or_paired.input_mate1 $single_or_paired.input_mate2 | 39 $single_or_paired.input_mate1 $single_or_paired.input_mate2 |
| 40 #end if | 40 #end if |
| 41 | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" output | 41 | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" - output |
| 42 ]]> | 42 ]]> |
| 43 </command> | 43 </command> |
| 44 <inputs> | 44 <inputs> |
| 45 <conditional name="referenceSource"> | 45 <conditional name="referenceSource"> |
| 46 <param name="source" type="select" label="Select a genome reference from your history or a built-in index?"> | 46 <param name="source" type="select" label="Select a genome reference from your history or a built-in index?"> |
| 81 <data name="output" format="bam" from_work_dir="output.bam" label="${tool.name} on ${on_string}" /> | 81 <data name="output" format="bam" from_work_dir="output.bam" label="${tool.name} on ${on_string}" /> |
| 82 </outputs> | 82 </outputs> |
| 83 <tests> | 83 <tests> |
| 84 <test> | 84 <test> |
| 85 <param name="referenceSource" value="history" /> | 85 <param name="referenceSource" value="history" /> |
| 86 <param name="reference" value="ref.fa" /> | 86 <param name="reference" value="ref.fa.gz" /> |
| 87 <param name="single_or_paired_opts" value="paired" /> | 87 <param name="single_or_paired_opts" value="paired" /> |
| 88 <param name="input_mate1" value="t_R1.fastq.gz" /> | 88 <param name="input_mate1" value="t_R1.fastq.gz" /> |
| 89 <param name="input_mate2" value="t_R2.fastq.gz" /> | 89 <param name="input_mate2" value="t_R2.fastq.gz" /> |
| 90 <output file="output.bam" ftype="bam" name="output" compare="sim_size" delta="10000"/> | 90 <output file="output.bam" ftype="bam" name="output" lines_diff="2"/> |
| 91 </test> | 91 </test> |
| 92 </tests> | 92 </tests> |
| 93 <help> | 93 <help> |
| 94 <![CDATA[ | 94 <![CDATA[ |
| 95 | 95 |