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comparison deepTools_macros.xml @ 14:b0d64a9930d6 draft

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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>