Mercurial > repos > thanhlv > bin3c
comparison mkmap.xml @ 17:1971cfa55ada draft
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 9f4ab03111185c7e20aaf669586278744713eee4
| author | thanhlv |
|---|---|
| date | Mon, 21 Oct 2019 05:26:18 -0400 |
| parents | cdfc397e7b0f |
| children | 327acdd0663d |
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| 16:cdfc397e7b0f | 17:1971cfa55ada |
|---|---|
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
| 7 <expand macro="version_command" /> | 7 <expand macro="version_command" /> |
| 8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
| 9 samtools sort -@ \${GALAXY_SLOTS:-1} -o sorted.bam -n $bam && | |
| 9 bin3C mkmap | 10 bin3C mkmap |
| 10 --min-extent $min_extent | 11 --min-extent $min_extent |
| 11 --min-reflen $min_reflen | 12 --min-reflen $min_reflen |
| 12 --min-signal $min_signal | 13 --min-signal $min_signal |
| 13 #if str($bin_size) != "0": | 14 #if str($bin_size) != "0": |
| 20 #if str($neb_name) != "": | 21 #if str($neb_name) != "": |
| 21 #for $enzyme in str($neb_name).split(',') | 22 #for $enzyme in str($neb_name).split(',') |
| 22 -e $enzyme | 23 -e $enzyme |
| 23 #end for | 24 #end for |
| 24 #end if | 25 #end if |
| 25 $ref $bam out | 26 $ref sorted.bam out |
| 26 ]]></command> | 27 ]]></command> |
| 27 | 28 |
| 28 <inputs> | 29 <inputs> |
| 29 <param name="ref" type="data" format="fasta,fastaq.gz" label="Reference fasta sequence" /> | 30 <param name="ref" type="data" format="fasta,fastaq.gz" label="Reference fasta sequence" /> |
| 30 <param name="bam" type="data" format="bam" label="Input bam file in query order" /> | 31 <param name="bam" type="data" format="bam" label="Input bam file in query order" /> |