annotate cuff_macros.xml @ 15:43b36b3d4333 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
author iuc
date Tue, 16 Jun 2020 13:00:02 -0400
parents d3ae7d9c2202
children af3e173cad7f
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
7
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
1 <macros>
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
2 <token name="@VERSION@">2.2.1</token>
13
f1b92120dfaa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 11
diff changeset
3
7
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
4 <xml name="requirements">
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
5 <requirements>
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
6 <requirement type="package" version="2.2.1">cufflinks</requirement>
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
7 <yield />
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
8 </requirements>
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
9 </xml>
13
f1b92120dfaa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 11
diff changeset
10
7
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
11 <xml name="condition_inputs">
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
12 <!-- DEFAULT : use BAM/SAM files -->
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
13 <conditional name="in_type">
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
14 <param name="set_in_type" type="select" label="Input data type"
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
15 help="CuffNorm supports either CXB (from cuffquant) or SAM/BAM input files. Mixing is not supported. Default: SAM/BAM">
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
16 <option value="BAM">SAM/BAM</option>
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
17 <option value="CXB">Cuffquant (CXB)</option>
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
18 <option value="CONDITION_LIST">List of single replicate conditions</option>
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
19 <option value="CONDITION_REPLICATE_LIST">List of multiple replicate conditions</option>
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
20 </param>
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
21 <when value="BAM">
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
22 <repeat name="conditions" title="Condition" min="2">
13
f1b92120dfaa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 11
diff changeset
23 <param name="name" label="Condition name" type="text"/>
7
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
24 <param name="samples" label="Replicates" type="data" format="sam,bam" multiple="true"/>
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
25 </repeat>
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
26 </when>
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
27 <when value="CXB">
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
28 <repeat name="conditions" title="Condition" min="2">
13
f1b92120dfaa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 11
diff changeset
29 <param name="name" label="Condition name" type="text"/>
7
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
30 <param name="samples" label="Replicates" type="data" format="cxb" multiple="true"/>
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
31 </repeat>
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
32 </when>
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
33 <when value="CONDITION_LIST">
13
f1b92120dfaa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 11
diff changeset
34 <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list" />
7
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
35 </when>
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
36 <when value="CONDITION_REPLICATE_LIST">
13
f1b92120dfaa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 11
diff changeset
37 <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list:list" />
7
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
38 </when>
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
39 </conditional>
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
40 </xml>
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
41 <token name="@CONDITION_SAMPLES@">
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
42 #if $in_type.set_in_type in ['BAM', 'CXB']
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
43 #for $condition in $in_type.conditions:
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
44 #set samples = ','.join( [ str( $sample ) for $sample in $condition.samples ] )
13
f1b92120dfaa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 11
diff changeset
45 '$samples'
7
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
46 #end for
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
47 #elif $in_type.set_in_type == 'CONDITION_LIST'
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
48 #for $sample in $in_type.conditions:
13
f1b92120dfaa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 11
diff changeset
49 '$sample'
7
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
50 #end for
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
51 #elif $in_type.set_in_type == 'CONDITION_REPLICATE_LIST'
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
52 #for $condition_list in $in_type.conditions:
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
53 #set samples = ','.join( [ str( $sample ) for $sample in $condition_list ] )
13
f1b92120dfaa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 11
diff changeset
54 '$samples'
7
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
55 #end for
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
56 #end if
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
57 </token>
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
58 <token name="@CONDITION_LABELS@">
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
59 #import re
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
60 #if $in_type.set_in_type in ['BAM', 'CXB']
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
61 #set labels = '\'' + '\',\''.join( [ str( $condition.name ) for $condition in $in_type.conditions ] ) + '\''
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
62 #elif $in_type.set_in_type in ['CONDITION_LIST', 'CONDITION_REPLICATE_LIST']
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
63 #set labels = '\'' + '\',\''.join( map(lambda x: re.sub('[^\w\-_]', '_', x), $in_type.conditions.keys() ) ) + '\''
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
64 #end if
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
65 --labels $labels
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
66 </token>
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
67 <xml name="cufflinks_gtf_inputs">
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
68 <param format="gtf" name="inputs" type="data" label="GTF file(s) produced by Cufflinks" help="" multiple="true" />
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
69 </xml>
15
43b36b3d4333 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
iuc
parents: 14
diff changeset
70 <token name="@CUFFLINKS_LINK_GTF_INPUTS@"><![CDATA[
43b36b3d4333 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
iuc
parents: 14
diff changeset
71 ## Inputs.
43b36b3d4333 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
iuc
parents: 14
diff changeset
72 #for $i, $input_file in enumerate($inputs):
43b36b3d4333 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
iuc
parents: 14
diff changeset
73 ln -s '${input_file}' input_$i &&
43b36b3d4333 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
iuc
parents: 14
diff changeset
74 #end for
43b36b3d4333 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
iuc
parents: 14
diff changeset
75 ]]></token>
7
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
76 <token name="@CUFFLINKS_GTF_INPUTS@">
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
77 ## Inputs.
15
43b36b3d4333 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
iuc
parents: 14
diff changeset
78 #for $i, $input_file in enumerate($inputs):
43b36b3d4333 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
iuc
parents: 14
diff changeset
79 'input_$i'
7
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
80 #end for
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
81 </token>
8da0eade1f59 Uploaded
devteam
parents:
diff changeset
82 <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token>
15
43b36b3d4333 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
iuc
parents: 14
diff changeset
83
43b36b3d4333 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
iuc
parents: 14
diff changeset
84 <xml name="citations">
43b36b3d4333 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
iuc
parents: 14
diff changeset
85 <citations>
43b36b3d4333 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
iuc
parents: 14
diff changeset
86 <citation type="doi">10.1038/nbt.1621</citation>
43b36b3d4333 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
iuc
parents: 14
diff changeset
87 <yield/>
43b36b3d4333 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
iuc
parents: 14
diff changeset
88 </citations>
43b36b3d4333 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
iuc
parents: 14
diff changeset
89 </xml>
43b36b3d4333 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
iuc
parents: 14
diff changeset
90
11
5ce5197de50c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
devteam
parents: 7
diff changeset
91 </macros>