Mercurial > repos > bgruening > deeptools
comparison deepTools_macros.xml @ 14:b0d64a9930d6 draft
Uploaded
| author | bgruening |
|---|---|
| date | Thu, 14 Nov 2013 05:43:15 -0500 |
| parents | 46ddfceb1bb2 |
| children | 351cd1f8791b |
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| 13:06311d89da81 | 14:b0d64a9930d6 |
|---|---|
| 66 .. _project site: https://github.com/fidelram/deepTools | 66 .. _project site: https://github.com/fidelram/deepTools |
| 67 | 67 |
| 68 </token> | 68 </token> |
| 69 | 69 |
| 70 <macro name="multiple_input_bams"> | 70 <macro name="multiple_input_bams"> |
| 71 <repeat name="inputs" title="Input files" min="2"> | 71 <repeat name="input_files" title="Input files" min="2"> |
| 72 <param name="bamfile" type="data" format="bam" | 72 <param name="bamfile" type="data" format="bam" |
| 73 label="Bam file" | 73 label="Bam file" |
| 74 help="The BAM file must be sorted."/> | 74 help="The BAM file must be sorted."/> |
| 75 <param name="label" type="text" size="30" optional="true" value="" | 75 <param name="label" type="text" size="30" optional="true" value="" |
| 76 label="Label" | 76 label="Label" |
| 77 help="Label to use in the output. If not given the dataset name will be used instead."/> | 77 help="Label to use in the output. If not given the dataset name will be used instead."/> |
| 78 </repeat> | 78 </repeat> |
| 79 </macro> | 79 </macro> |
| 80 | |
| 81 <token name="@multiple_input_bams@"> | |
| 82 #for $i in $input_files: | |
| 83 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) | |
| 84 #set $temp_input_path = $temp_input_handle.name | |
| 85 #silent $temp_input_handle.close() | |
| 86 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path)) | |
| 87 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path)) | |
| 88 #silent $files.append('%s.bam' % $temp_input_path) | |
| 89 | |
| 90 ##set $files += [str($i.bamfile)] | |
| 91 #if str($i.label.value) != "": | |
| 92 #set $labels += ["\"%s\"" % ($i.label.value)] | |
| 93 #else | |
| 94 #set $labels += ["\"%s\"" % ($i.bamfile.name)] | |
| 95 #end if | |
| 96 #end for | |
| 97 </token> | |
| 80 | 98 |
| 81 <macro name="reference_genome_source"> | 99 <macro name="reference_genome_source"> |
| 82 <conditional name="source"> | 100 <conditional name="source"> |
| 83 <param name="ref_source" type="select" label="Reference genome"> | 101 <param name="ref_source" type="select" label="Reference genome"> |
| 84 <option value="cached">locally cached</option> | 102 <option value="cached">locally cached</option> |