Mercurial > repos > devteam > cuffdiff
annotate cuff_macros.xml @ 3:9ec1cc10742c draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
author | devteam |
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date | Tue, 07 Feb 2017 18:38:03 -0500 |
parents | 9ba750f285e3 |
children | e20b05db0839 |
rev | line source |
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0 | 1 <macros> |
2 <token name="@VERSION@">2.2.1</token> | |
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9ec1cc10742c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
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3 |
0 | 4 <xml name="requirements"> |
5 <requirements> | |
6 <requirement type="package" version="2.2.1">cufflinks</requirement> | |
7 <yield /> | |
8 </requirements> | |
9 </xml> | |
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9ec1cc10742c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents:
1
diff
changeset
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10 |
0 | 11 <xml name="stdio"> |
12 <stdio> | |
13 <exit_code range="1:" /> | |
14 <exit_code range=":-1" /> | |
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9ba750f285e3
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
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diff
changeset
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15 <regex match="Error" /> |
9ba750f285e3
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
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16 <regex match="Exception" /> |
0 | 17 </stdio> |
18 </xml> | |
19 <xml name="condition_inputs"> | |
20 <!-- DEFAULT : use BAM/SAM files --> | |
21 <conditional name="in_type"> | |
22 <param name="set_in_type" type="select" label="Input data type" | |
23 help="CuffNorm supports either CXB (from cuffquant) or SAM/BAM input files. Mixing is not supported. Default: SAM/BAM"> | |
24 <option value="BAM">SAM/BAM</option> | |
25 <option value="CXB">Cuffquant (CXB)</option> | |
26 <option value="CONDITION_LIST">List of single replicate conditions</option> | |
27 <option value="CONDITION_REPLICATE_LIST">List of multiple replicate conditions</option> | |
28 </param> | |
29 <when value="BAM"> | |
30 <repeat name="conditions" title="Condition" min="2"> | |
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9ec1cc10742c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents:
1
diff
changeset
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31 <param name="name" label="Condition name" type="text"/> |
0 | 32 <param name="samples" label="Replicates" type="data" format="sam,bam" multiple="true"/> |
33 </repeat> | |
34 </when> | |
35 <when value="CXB"> | |
36 <repeat name="conditions" title="Condition" min="2"> | |
3
9ec1cc10742c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents:
1
diff
changeset
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37 <param name="name" label="Condition name" type="text"/> |
0 | 38 <param name="samples" label="Replicates" type="data" format="cxb" multiple="true"/> |
39 </repeat> | |
40 </when> | |
41 <when value="CONDITION_LIST"> | |
3
9ec1cc10742c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents:
1
diff
changeset
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42 <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list" /> |
0 | 43 </when> |
44 <when value="CONDITION_REPLICATE_LIST"> | |
3
9ec1cc10742c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents:
1
diff
changeset
|
45 <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list:list" /> |
0 | 46 </when> |
47 </conditional> | |
48 </xml> | |
49 <token name="@CONDITION_SAMPLES@"> | |
50 #if $in_type.set_in_type in ['BAM', 'CXB'] | |
51 #for $condition in $in_type.conditions: | |
52 #set samples = ','.join( [ str( $sample ) for $sample in $condition.samples ] ) | |
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9ec1cc10742c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents:
1
diff
changeset
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53 '$samples' |
0 | 54 #end for |
55 #elif $in_type.set_in_type == 'CONDITION_LIST' | |
56 #for $sample in $in_type.conditions: | |
3
9ec1cc10742c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents:
1
diff
changeset
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57 '$sample' |
0 | 58 #end for |
59 #elif $in_type.set_in_type == 'CONDITION_REPLICATE_LIST' | |
60 #for $condition_list in $in_type.conditions: | |
61 #set samples = ','.join( [ str( $sample ) for $sample in $condition_list ] ) | |
3
9ec1cc10742c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents:
1
diff
changeset
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62 '$samples' |
0 | 63 #end for |
64 #end if | |
65 </token> | |
66 <token name="@CONDITION_LABELS@"> | |
67 #import re | |
68 #if $in_type.set_in_type in ['BAM', 'CXB'] | |
69 #set labels = '\'' + '\',\''.join( [ str( $condition.name ) for $condition in $in_type.conditions ] ) + '\'' | |
70 #elif $in_type.set_in_type in ['CONDITION_LIST', 'CONDITION_REPLICATE_LIST'] | |
71 #set labels = '\'' + '\',\''.join( map(lambda x: re.sub('[^\w\-_]', '_', x), $in_type.conditions.keys() ) ) + '\'' | |
72 #end if | |
73 --labels $labels | |
74 </token> | |
75 <xml name="cufflinks_gtf_inputs"> | |
76 <param format="gtf" name="inputs" type="data" label="GTF file(s) produced by Cufflinks" help="" multiple="true" /> | |
77 <repeat name="additional_inputs" title="Additional GTF Inputs (Lists)"> | |
78 <param format="gtf" name="additional_inputs" type="data_collection" label="GTF file(s) produced by Cufflinks" help="" /> | |
79 </repeat> | |
80 </xml> | |
81 <token name="@CUFFLINKS_GTF_INPUTS@"> | |
82 ## Inputs. | |
83 #for $input_file in $inputs: | |
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9ec1cc10742c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents:
1
diff
changeset
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84 '${input_file}' |
0 | 85 #end for |
86 #for $additional_input in $additional_inputs: | |
87 #for $input_file in $additional_input.additional_inputs: | |
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9ec1cc10742c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents:
1
diff
changeset
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88 '${input_file}' |
0 | 89 #end for |
90 #end for | |
91 </token> | |
92 <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token> | |
1
9ba750f285e3
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
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93 </macros> |