Mercurial > repos > fubar > htseq_bams_to_count_matrix
comparison htseqsams2mx.xml @ 49:c57e63d1a9d2 draft
working test. first upload
| author | fubar |
|---|---|
| date | Fri, 02 Jan 2015 03:32:39 -0500 |
| parents | edda3a085658 |
| children |
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| 48:58fe9656873a | 49:c57e63d1a9d2 |
|---|---|
| 8 <requirement type="package" version="1.2.1">matplotlib</requirement> | 8 <requirement type="package" version="1.2.1">matplotlib</requirement> |
| 9 <requirement type="package" version="0.5.4p3">htseq</requirement> | 9 <requirement type="package" version="0.5.4p3">htseq</requirement> |
| 10 </requirements> | 10 </requirements> |
| 11 <command interpreter="python"> | 11 <command interpreter="python"> |
| 12 htseqsams2mx.py -g "$gfffile" -o "$outfile" -m "$model" --id_attribute "$id_attr" --feature_type "$feature_type" | 12 htseqsams2mx.py -g "$gfffile" -o "$outfile" -m "$model" --id_attribute "$id_attr" --feature_type "$feature_type" |
| 13 --mapqMin $mapqMin --samf "'${firstsamf}','${firstsamf.name}','${firstsamf.ext}','${firstsamf.metadata.bam_index}'" | 13 --mapqMin $mapqMin |
| 14 #if $secondsamf.ext != 'data': | |
| 15 --samf "'${secondsamf}','${secondsamf.name}','${secondsamf.ext}','${secondsamf.metadata.bam_index}'" | |
| 16 #end if | |
| 17 #for $s in $samfiles: | 14 #for $s in $samfiles: |
| 18 #if $s.samf.ext != 'data': | 15 #if $s.ext != 'data': |
| 19 --samf "'${s.samf}','${s.samf.name}','${s.samf.ext}','${s.samf.metadata.bam_index}'" | 16 --samf "'${s}','${s.name}','${s.ext}','${s.metadata.bam_index}'" |
| 20 #end if | 17 #end if |
| 21 #end for | 18 #end for |
| 22 #if $filter_extras: | 19 #if $filter_extras: |
| 23 --filter_extras "$filter_extras" | 20 --filter_extras "$filter_extras" |
| 24 #end if | 21 #end if |
| 56 <option value="">None</option> | 53 <option value="">None</option> |
| 57 <option value="XS">XS:i > 0 - More than one mapping position Bowtie</option> | 54 <option value="XS">XS:i > 0 - More than one mapping position Bowtie</option> |
| 58 <option value="XS:A">Might be useful for tophat</option> | 55 <option value="XS:A">Might be useful for tophat</option> |
| 59 </param> | 56 </param> |
| 60 | 57 |
| 61 <param name="firstsamf" type="data" label="bam/sam file from your history" format="sam,bam" size="100" | 58 <param name="samfiles" type="data" label="bam/sam file from your history" format="sam,bam" size="100" multiple="true"/> |
| 62 help="Each sam/bam contributes a column of read counts overlapping the specified gene model contigs" | |
| 63 optional="false"/> | |
| 64 <param name="secondsamf" type="data" label="Additional bam/sam file from your history" format="sam,bam" size="100" | |
| 65 help="Each sam/bam contributes a column of read counts overlapping the specified gene model contigs" | |
| 66 optional="false"/> | |
| 67 <repeat name="samfiles" min="16" | |
| 68 title="Specify additional bam/sam file inputs" help="Each sam/bam contributes a column of read counts overlapping the specified gene model contigs"> | |
| 69 <param name="samf" type="data" label="Additional bam/sam file from your history" format="sam,bam" size="100" | |
| 70 optional="true"/> | |
| 71 </repeat> | |
| 72 </inputs> | 59 </inputs> |
| 73 <outputs> | 60 <outputs> |
| 74 <data format="tabular" name="outfile" label="${title}_htseqsams2mx.xls" /> | 61 <data format="tabular" name="outfile" label="${title}_htseqsams2mx.xls" /> |
| 75 </outputs> | 62 </outputs> |
| 76 <tests> | 63 <tests> |
| 77 <test> | 64 <test> |
| 78 <param name="feature_type" value="exon" /> | 65 <param name="feature_type" value="exon" /> |
| 79 <param name="gfffile" value="rn4_chr20_100k.gtf" /> | 66 <param name="gfffile" value="rn4_chr20_100k.gtf" /> |
| 80 <param name="firstsamf" value="rn4chr20test1.bam" ftype="bam"/> | 67 <param name="samfiles" value="rn4chr20test1.bam,rn4chr20test2.bam" ftype="bam"/> |
| 81 <param name="secondsamf" value="rn4chr20test2.bam" ftype="bam"/> | |
| 82 <param name="id_attr" value="gene_name" /> | 68 <param name="id_attr" value="gene_name" /> |
| 83 <param name="model" value="union" /> | 69 <param name="model" value="union" /> |
| 84 <param name="stranded" value="no" /> | 70 <param name="stranded" value="no" /> |
| 85 <param name="title" value="htseqtest" /> | 71 <param name="title" value="htseqtest" /> |
| 86 <param name="mapqMin" value="0" /> | 72 <param name="mapqMin" value="0" /> |