Mercurial > repos > devteam > cuffnorm
comparison cuff_macros.xml @ 5:9a854107dbb2 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm commit 6b66cbbde16c35593fe95066ea2b91623bf35140"
author | iuc |
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date | Fri, 03 Jul 2020 11:44:40 -0400 |
parents | 6cbfede05833 |
children | 28b94cfbfdb9 |
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4:6cbfede05833 | 5:9a854107dbb2 |
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1 <macros> | 1 <macros> |
2 <token name="@VERSION@">2.2.1</token> | 2 <token name="@VERSION@">2.2.1</token> |
3 | 3 |
4 <xml name="requirements"> | 4 <xml name="requirements"> |
5 <requirements> | 5 <requirements> |
6 <requirement type="package" version="2.2.1">cufflinks</requirement> | 6 <requirement type="package" version="2.2.1">cufflinks</requirement> |
7 <yield /> | 7 <yield /> |
8 </requirements> | 8 </requirements> |
9 </xml> | 9 </xml> |
10 | 10 |
11 <xml name="condition_inputs"> | 11 <xml name="conditions_repeat" token_format=""> |
12 <!-- DEFAULT : use BAM/SAM files --> | 12 <repeat name="conditions" title="Condition" min="2"> |
13 <conditional name="in_type"> | 13 <param name="name" label="Condition name" type="text"> |
14 <param name="set_in_type" type="select" label="Input data type" | 14 <validator type="empty_field" message="You must provide a condition name" /> |
15 help="CuffNorm supports either CXB (from cuffquant) or SAM/BAM input files. Mixing is not supported. Default: SAM/BAM"> | 15 <validator type="expression" message="Commas are not allowed in condition names">value and "," not in value</validator> |
16 <option value="BAM">SAM/BAM</option> | 16 </param> |
17 <option value="CXB">Cuffquant (CXB)</option> | 17 <param name="samples" label="Replicates" type="data" format="@FORMAT@" multiple="true"/> |
18 <option value="CONDITION_LIST">List of single replicate conditions</option> | 18 </repeat> |
19 <option value="CONDITION_REPLICATE_LIST">List of multiple replicate conditions</option> | 19 </xml> |
20 </param> | |
21 <when value="BAM"> | |
22 <repeat name="conditions" title="Condition" min="2"> | |
23 <param name="name" label="Condition name" type="text"/> | |
24 <param name="samples" label="Replicates" type="data" format="sam,bam" multiple="true"/> | |
25 </repeat> | |
26 </when> | |
27 <when value="CXB"> | |
28 <repeat name="conditions" title="Condition" min="2"> | |
29 <param name="name" label="Condition name" type="text"/> | |
30 <param name="samples" label="Replicates" type="data" format="cxb" multiple="true"/> | |
31 </repeat> | |
32 </when> | |
33 <when value="CONDITION_LIST"> | |
34 <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list" /> | |
35 </when> | |
36 <when value="CONDITION_REPLICATE_LIST"> | |
37 <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list:list" /> | |
38 </when> | |
39 </conditional> | |
40 </xml> | |
41 <token name="@CONDITION_SAMPLES@"> | |
42 #if $in_type.set_in_type in ['BAM', 'CXB'] | |
43 #for $condition in $in_type.conditions: | |
44 #set samples = ','.join( [ str( $sample ) for $sample in $condition.samples ] ) | |
45 '$samples' | |
46 #end for | |
47 #elif $in_type.set_in_type == 'CONDITION_LIST' | |
48 #for $sample in $in_type.conditions: | |
49 '$sample' | |
50 #end for | |
51 #elif $in_type.set_in_type == 'CONDITION_REPLICATE_LIST' | |
52 #for $condition_list in $in_type.conditions: | |
53 #set samples = ','.join( [ str( $sample ) for $sample in $condition_list ] ) | |
54 '$samples' | |
55 #end for | |
56 #end if | |
57 </token> | |
58 <token name="@CONDITION_LABELS@"> | |
59 #import re | |
60 #if $in_type.set_in_type in ['BAM', 'CXB'] | |
61 #set labels = '\'' + '\',\''.join( [ str( $condition.name ) for $condition in $in_type.conditions ] ) + '\'' | |
62 #elif $in_type.set_in_type in ['CONDITION_LIST', 'CONDITION_REPLICATE_LIST'] | |
63 #set labels = '\'' + '\',\''.join( map(lambda x: re.sub('[^\w\-_]', '_', x), $in_type.conditions.keys() ) ) + '\'' | |
64 #end if | |
65 --labels $labels | |
66 </token> | |
67 <xml name="cufflinks_gtf_inputs"> | |
68 <param format="gtf" name="inputs" type="data" label="GTF file(s) produced by Cufflinks" help="" multiple="true" /> | |
69 </xml> | |
70 <token name="@CUFFLINKS_LINK_GTF_INPUTS@"><![CDATA[ | |
71 ## Inputs. | |
72 #for $i, $input_file in enumerate($inputs): | |
73 ln -s '${input_file}' input_$i && | |
74 #end for | |
75 ]]></token> | |
76 <token name="@CUFFLINKS_GTF_INPUTS@"> | |
77 ## Inputs. | |
78 #for $i, $input_file in enumerate($inputs): | |
79 'input_$i' | |
80 #end for | |
81 </token> | |
82 <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token> | |
83 | 20 |
84 <xml name="citations"> | 21 <xml name="condition_inputs"> |
85 <citations> | 22 <!-- DEFAULT : use BAM/SAM files --> |
86 <citation type="doi">10.1038/nbt.1621</citation> | 23 <conditional name="in_type"> |
87 <yield/> | 24 <param name="set_in_type" type="select" label="Input data type" |
88 </citations> | 25 help="CuffNorm supports either CXB (from cuffquant) or SAM/BAM input files. Mixing is not supported. Default: SAM/BAM"> |
89 </xml> | 26 <option value="BAM">SAM/BAM</option> |
27 <option value="CXB">Cuffquant (CXB)</option> | |
28 <option value="CONDITION_LIST">List of single replicate conditions</option> | |
29 <option value="CONDITION_REPLICATE_LIST">List of multiple replicate conditions</option> | |
30 </param> | |
31 <when value="BAM"> | |
32 <expand macro="conditions_repeat" format="sam,bam" /> | |
33 </when> | |
34 <when value="CXB"> | |
35 <expand macro="conditions_repeat" format="cxb" /> | |
36 </when> | |
37 <when value="CONDITION_LIST"> | |
38 <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list" /> | |
39 </when> | |
40 <when value="CONDITION_REPLICATE_LIST"> | |
41 <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list:list" /> | |
42 </when> | |
43 </conditional> | |
44 </xml> | |
45 <token name="@CONDITION_SAMPLES@"><![CDATA[ | |
46 #if $in_type.set_in_type in ['BAM', 'CXB'] | |
47 #for $condition in $in_type.conditions: | |
48 #set samples = ','.join([str($sample) for $sample in $condition.samples]) | |
49 '$samples' | |
50 #end for | |
51 #elif $in_type.set_in_type == 'CONDITION_LIST' | |
52 #for $sample in $in_type.conditions: | |
53 '$sample' | |
54 #end for | |
55 #elif $in_type.set_in_type == 'CONDITION_REPLICATE_LIST' | |
56 #for $condition_list in $in_type.conditions: | |
57 #set samples = ','.join([str($sample) for $sample in $condition_list]) | |
58 '$samples' | |
59 #end for | |
60 #end if | |
61 ]]></token> | |
62 <token name="@CONDITION_LABELS@"><![CDATA[ | |
63 #import re | |
64 #if $in_type.set_in_type in ['BAM', 'CXB'] | |
65 #set labels = "','".join([str($condition.name) for $condition in $in_type.conditions]) | |
66 #elif $in_type.set_in_type in ['CONDITION_LIST', 'CONDITION_REPLICATE_LIST'] | |
67 #set labels = "','".join([str($condition).replace(',', '_') for $condition in $in_type.conditions.keys()]) | |
68 #end if | |
69 --labels '$labels' | |
70 ]]></token> | |
71 <xml name="cufflinks_gtf_inputs"> | |
72 <param format="gtf" name="inputs" type="data" label="GTF file(s) produced by Cufflinks" help="" multiple="true" /> | |
73 </xml> | |
74 <token name="@CUFFLINKS_LINK_GTF_INPUTS@"><![CDATA[ | |
75 ## Inputs. | |
76 #for $i, $input_file in enumerate($inputs): | |
77 ln -s '${input_file}' input_$i && | |
78 #end for | |
79 ]]></token> | |
80 <token name="@CUFFLINKS_GTF_INPUTS@"><![CDATA[ | |
81 ## Inputs. | |
82 #for $i, $input_file in enumerate($inputs): | |
83 'input_$i' | |
84 #end for | |
85 ]]></token> | |
86 <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token> | |
87 | |
88 <xml name="citations"> | |
89 <citations> | |
90 <citation type="doi">10.1038/nbt.1621</citation> | |
91 <yield/> | |
92 </citations> | |
93 </xml> | |
90 | 94 |
91 </macros> | 95 </macros> |