annotate cuff_macros.xml @ 2:f8fdf50e0b3b draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffnorm commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
author devteam
date Tue, 07 Feb 2017 18:40:18 -0500
parents 7d4c2097aac5
children f5b2ee725d34
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a26af05ac218 Uploaded
devteam
parents:
diff changeset
1 <macros>
a26af05ac218 Uploaded
devteam
parents:
diff changeset
2 <token name="@VERSION@">2.2.1</token>
2
f8fdf50e0b3b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffnorm commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 1
diff changeset
3
0
a26af05ac218 Uploaded
devteam
parents:
diff changeset
4 <xml name="requirements">
a26af05ac218 Uploaded
devteam
parents:
diff changeset
5 <requirements>
a26af05ac218 Uploaded
devteam
parents:
diff changeset
6 <requirement type="package" version="2.2.1">cufflinks</requirement>
a26af05ac218 Uploaded
devteam
parents:
diff changeset
7 <yield />
a26af05ac218 Uploaded
devteam
parents:
diff changeset
8 </requirements>
a26af05ac218 Uploaded
devteam
parents:
diff changeset
9 </xml>
2
f8fdf50e0b3b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffnorm commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 1
diff changeset
10
0
a26af05ac218 Uploaded
devteam
parents:
diff changeset
11 <xml name="stdio">
a26af05ac218 Uploaded
devteam
parents:
diff changeset
12 <stdio>
a26af05ac218 Uploaded
devteam
parents:
diff changeset
13 <exit_code range="1:" />
a26af05ac218 Uploaded
devteam
parents:
diff changeset
14 <exit_code range=":-1" />
1
7d4c2097aac5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffnorm commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 0
diff changeset
15 <regex match="Error" />
7d4c2097aac5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffnorm commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 0
diff changeset
16 <regex match="Exception" />
0
a26af05ac218 Uploaded
devteam
parents:
diff changeset
17 </stdio>
a26af05ac218 Uploaded
devteam
parents:
diff changeset
18 </xml>
a26af05ac218 Uploaded
devteam
parents:
diff changeset
19 <xml name="condition_inputs">
a26af05ac218 Uploaded
devteam
parents:
diff changeset
20 <!-- DEFAULT : use BAM/SAM files -->
a26af05ac218 Uploaded
devteam
parents:
diff changeset
21 <conditional name="in_type">
a26af05ac218 Uploaded
devteam
parents:
diff changeset
22 <param name="set_in_type" type="select" label="Input data type"
a26af05ac218 Uploaded
devteam
parents:
diff changeset
23 help="CuffNorm supports either CXB (from cuffquant) or SAM/BAM input files. Mixing is not supported. Default: SAM/BAM">
a26af05ac218 Uploaded
devteam
parents:
diff changeset
24 <option value="BAM">SAM/BAM</option>
a26af05ac218 Uploaded
devteam
parents:
diff changeset
25 <option value="CXB">Cuffquant (CXB)</option>
a26af05ac218 Uploaded
devteam
parents:
diff changeset
26 <option value="CONDITION_LIST">List of single replicate conditions</option>
a26af05ac218 Uploaded
devteam
parents:
diff changeset
27 <option value="CONDITION_REPLICATE_LIST">List of multiple replicate conditions</option>
a26af05ac218 Uploaded
devteam
parents:
diff changeset
28 </param>
a26af05ac218 Uploaded
devteam
parents:
diff changeset
29 <when value="BAM">
a26af05ac218 Uploaded
devteam
parents:
diff changeset
30 <repeat name="conditions" title="Condition" min="2">
2
f8fdf50e0b3b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffnorm commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 1
diff changeset
31 <param name="name" label="Condition name" type="text"/>
0
a26af05ac218 Uploaded
devteam
parents:
diff changeset
32 <param name="samples" label="Replicates" type="data" format="sam,bam" multiple="true"/>
a26af05ac218 Uploaded
devteam
parents:
diff changeset
33 </repeat>
a26af05ac218 Uploaded
devteam
parents:
diff changeset
34 </when>
a26af05ac218 Uploaded
devteam
parents:
diff changeset
35 <when value="CXB">
a26af05ac218 Uploaded
devteam
parents:
diff changeset
36 <repeat name="conditions" title="Condition" min="2">
2
f8fdf50e0b3b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffnorm commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 1
diff changeset
37 <param name="name" label="Condition name" type="text"/>
0
a26af05ac218 Uploaded
devteam
parents:
diff changeset
38 <param name="samples" label="Replicates" type="data" format="cxb" multiple="true"/>
a26af05ac218 Uploaded
devteam
parents:
diff changeset
39 </repeat>
a26af05ac218 Uploaded
devteam
parents:
diff changeset
40 </when>
a26af05ac218 Uploaded
devteam
parents:
diff changeset
41 <when value="CONDITION_LIST">
2
f8fdf50e0b3b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffnorm commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 1
diff changeset
42 <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list" />
0
a26af05ac218 Uploaded
devteam
parents:
diff changeset
43 </when>
a26af05ac218 Uploaded
devteam
parents:
diff changeset
44 <when value="CONDITION_REPLICATE_LIST">
2
f8fdf50e0b3b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffnorm commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 1
diff changeset
45 <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list:list" />
0
a26af05ac218 Uploaded
devteam
parents:
diff changeset
46 </when>
a26af05ac218 Uploaded
devteam
parents:
diff changeset
47 </conditional>
a26af05ac218 Uploaded
devteam
parents:
diff changeset
48 </xml>
a26af05ac218 Uploaded
devteam
parents:
diff changeset
49 <token name="@CONDITION_SAMPLES@">
a26af05ac218 Uploaded
devteam
parents:
diff changeset
50 #if $in_type.set_in_type in ['BAM', 'CXB']
a26af05ac218 Uploaded
devteam
parents:
diff changeset
51 #for $condition in $in_type.conditions:
a26af05ac218 Uploaded
devteam
parents:
diff changeset
52 #set samples = ','.join( [ str( $sample ) for $sample in $condition.samples ] )
2
f8fdf50e0b3b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffnorm commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 1
diff changeset
53 '$samples'
0
a26af05ac218 Uploaded
devteam
parents:
diff changeset
54 #end for
a26af05ac218 Uploaded
devteam
parents:
diff changeset
55 #elif $in_type.set_in_type == 'CONDITION_LIST'
a26af05ac218 Uploaded
devteam
parents:
diff changeset
56 #for $sample in $in_type.conditions:
2
f8fdf50e0b3b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffnorm commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 1
diff changeset
57 '$sample'
0
a26af05ac218 Uploaded
devteam
parents:
diff changeset
58 #end for
a26af05ac218 Uploaded
devteam
parents:
diff changeset
59 #elif $in_type.set_in_type == 'CONDITION_REPLICATE_LIST'
a26af05ac218 Uploaded
devteam
parents:
diff changeset
60 #for $condition_list in $in_type.conditions:
a26af05ac218 Uploaded
devteam
parents:
diff changeset
61 #set samples = ','.join( [ str( $sample ) for $sample in $condition_list ] )
2
f8fdf50e0b3b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffnorm commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 1
diff changeset
62 '$samples'
0
a26af05ac218 Uploaded
devteam
parents:
diff changeset
63 #end for
a26af05ac218 Uploaded
devteam
parents:
diff changeset
64 #end if
a26af05ac218 Uploaded
devteam
parents:
diff changeset
65 </token>
a26af05ac218 Uploaded
devteam
parents:
diff changeset
66 <token name="@CONDITION_LABELS@">
a26af05ac218 Uploaded
devteam
parents:
diff changeset
67 #import re
a26af05ac218 Uploaded
devteam
parents:
diff changeset
68 #if $in_type.set_in_type in ['BAM', 'CXB']
a26af05ac218 Uploaded
devteam
parents:
diff changeset
69 #set labels = '\'' + '\',\''.join( [ str( $condition.name ) for $condition in $in_type.conditions ] ) + '\''
a26af05ac218 Uploaded
devteam
parents:
diff changeset
70 #elif $in_type.set_in_type in ['CONDITION_LIST', 'CONDITION_REPLICATE_LIST']
a26af05ac218 Uploaded
devteam
parents:
diff changeset
71 #set labels = '\'' + '\',\''.join( map(lambda x: re.sub('[^\w\-_]', '_', x), $in_type.conditions.keys() ) ) + '\''
a26af05ac218 Uploaded
devteam
parents:
diff changeset
72 #end if
a26af05ac218 Uploaded
devteam
parents:
diff changeset
73 --labels $labels
a26af05ac218 Uploaded
devteam
parents:
diff changeset
74 </token>
a26af05ac218 Uploaded
devteam
parents:
diff changeset
75 <xml name="cufflinks_gtf_inputs">
a26af05ac218 Uploaded
devteam
parents:
diff changeset
76 <param format="gtf" name="inputs" type="data" label="GTF file(s) produced by Cufflinks" help="" multiple="true" />
a26af05ac218 Uploaded
devteam
parents:
diff changeset
77 <repeat name="additional_inputs" title="Additional GTF Inputs (Lists)">
a26af05ac218 Uploaded
devteam
parents:
diff changeset
78 <param format="gtf" name="additional_inputs" type="data_collection" label="GTF file(s) produced by Cufflinks" help="" />
a26af05ac218 Uploaded
devteam
parents:
diff changeset
79 </repeat>
a26af05ac218 Uploaded
devteam
parents:
diff changeset
80 </xml>
a26af05ac218 Uploaded
devteam
parents:
diff changeset
81 <token name="@CUFFLINKS_GTF_INPUTS@">
a26af05ac218 Uploaded
devteam
parents:
diff changeset
82 ## Inputs.
a26af05ac218 Uploaded
devteam
parents:
diff changeset
83 #for $input_file in $inputs:
2
f8fdf50e0b3b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffnorm commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 1
diff changeset
84 '${input_file}'
0
a26af05ac218 Uploaded
devteam
parents:
diff changeset
85 #end for
a26af05ac218 Uploaded
devteam
parents:
diff changeset
86 #for $additional_input in $additional_inputs:
a26af05ac218 Uploaded
devteam
parents:
diff changeset
87 #for $input_file in $additional_input.additional_inputs:
2
f8fdf50e0b3b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffnorm commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 1
diff changeset
88 '${input_file}'
0
a26af05ac218 Uploaded
devteam
parents:
diff changeset
89 #end for
a26af05ac218 Uploaded
devteam
parents:
diff changeset
90 #end for
a26af05ac218 Uploaded
devteam
parents:
diff changeset
91 </token>
a26af05ac218 Uploaded
devteam
parents:
diff changeset
92 <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token>
1
7d4c2097aac5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffnorm commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 0
diff changeset
93 </macros>