annotate cuff_macros.xml @ 11:e04dbae2abe0 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
author devteam
date Sun, 19 Feb 2017 12:12:28 -0500
parents 83bec71c5c9f
children d080005cffe1
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
7
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
1 <macros>
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
2 <token name="@VERSION@">2.2.1</token>
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 9
diff changeset
3
7
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
4 <xml name="requirements">
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
5 <requirements>
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
6 <requirement type="package" version="2.2.1">cufflinks</requirement>
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
7 <yield />
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
8 </requirements>
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
9 </xml>
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 9
diff changeset
10
7
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
11 <xml name="condition_inputs">
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
12 <!-- DEFAULT : use BAM/SAM files -->
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
13 <conditional name="in_type">
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
14 <param name="set_in_type" type="select" label="Input data type"
5346d5eea8b1 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">
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
16 <option value="BAM">SAM/BAM</option>
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
17 <option value="CXB">Cuffquant (CXB)</option>
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
18 <option value="CONDITION_LIST">List of single replicate conditions</option>
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
19 <option value="CONDITION_REPLICATE_LIST">List of multiple replicate conditions</option>
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
20 </param>
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
21 <when value="BAM">
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
22 <repeat name="conditions" title="Condition" min="2">
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 9
diff changeset
23 <param name="name" label="Condition name" type="text"/>
7
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
24 <param name="samples" label="Replicates" type="data" format="sam,bam" multiple="true"/>
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
25 </repeat>
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
26 </when>
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
27 <when value="CXB">
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
28 <repeat name="conditions" title="Condition" min="2">
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 9
diff changeset
29 <param name="name" label="Condition name" type="text"/>
7
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
30 <param name="samples" label="Replicates" type="data" format="cxb" multiple="true"/>
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
31 </repeat>
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
32 </when>
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
33 <when value="CONDITION_LIST">
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 9
diff changeset
34 <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list" />
7
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
35 </when>
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
36 <when value="CONDITION_REPLICATE_LIST">
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 9
diff changeset
37 <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list:list" />
7
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
38 </when>
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
39 </conditional>
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
40 </xml>
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
41 <token name="@CONDITION_SAMPLES@">
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
42 #if $in_type.set_in_type in ['BAM', 'CXB']
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
43 #for $condition in $in_type.conditions:
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
44 #set samples = ','.join( [ str( $sample ) for $sample in $condition.samples ] )
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 9
diff changeset
45 '$samples'
7
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
46 #end for
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
47 #elif $in_type.set_in_type == 'CONDITION_LIST'
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
48 #for $sample in $in_type.conditions:
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 9
diff changeset
49 '$sample'
7
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
50 #end for
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
51 #elif $in_type.set_in_type == 'CONDITION_REPLICATE_LIST'
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
52 #for $condition_list in $in_type.conditions:
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
53 #set samples = ','.join( [ str( $sample ) for $sample in $condition_list ] )
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 9
diff changeset
54 '$samples'
7
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
55 #end for
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
56 #end if
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
57 </token>
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
58 <token name="@CONDITION_LABELS@">
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
59 #import re
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
60 #if $in_type.set_in_type in ['BAM', 'CXB']
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
61 #set labels = '\'' + '\',\''.join( [ str( $condition.name ) for $condition in $in_type.conditions ] ) + '\''
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
62 #elif $in_type.set_in_type in ['CONDITION_LIST', 'CONDITION_REPLICATE_LIST']
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
63 #set labels = '\'' + '\',\''.join( map(lambda x: re.sub('[^\w\-_]', '_', x), $in_type.conditions.keys() ) ) + '\''
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
64 #end if
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
65 --labels $labels
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
66 </token>
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
67 <xml name="cufflinks_gtf_inputs">
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
68 <param format="gtf" name="inputs" type="data" label="GTF file(s) produced by Cufflinks" help="" multiple="true" />
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
69 <repeat name="additional_inputs" title="Additional GTF Inputs (Lists)">
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
70 <param format="gtf" name="additional_inputs" type="data_collection" label="GTF file(s) produced by Cufflinks" help="" />
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
71 </repeat>
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
72 </xml>
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
73 <token name="@CUFFLINKS_GTF_INPUTS@">
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
74 ## Inputs.
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
75 #for $input_file in $inputs:
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 9
diff changeset
76 '${input_file}'
7
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
77 #end for
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
78 #for $additional_input in $additional_inputs:
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
79 #for $input_file in $additional_input.additional_inputs:
10
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 9
diff changeset
80 '${input_file}'
7
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
81 #end for
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
82 #end for
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
83 </token>
5346d5eea8b1 Uploaded
devteam
parents:
diff changeset
84 <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token>
9
a1ea9af8d5f4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 7
diff changeset
85 </macros>