Mercurial > repos > iuc > meme_fimo

annotate fimo.xml @ 12:e37874b1f811 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
author iuc
date Thu, 17 May 2018 14:09:34 -0400
parents ce2feec4c8d2
children daf857eed38f
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
10
ce2feec4c8d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents: 9
diff changeset
1 <tool id="meme_fimo" name="FIMO" version="@WRAPPER_VERSION@.0">
12
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
2 <description>- Scan a set of sequences for motifs</description>
9
b69b8c6bbbde planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents: 7
diff changeset
3 <macros>
b69b8c6bbbde planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents: 7
diff changeset
4 <import>macros.xml</import>
b69b8c6bbbde planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents: 7
diff changeset
5 </macros>
b69b8c6bbbde planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents: 7
diff changeset
6 <expand macro="requirements" />
b69b8c6bbbde planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents: 7
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
12
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
8 fimo
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
9 -o ./out/
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
10 $scanrc
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
11 #if str( $options_type.options_type_selector ) == 'advanced':
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
12 --thresh $options_type.thresh
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
13 $options_type.qv_thresh
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
14 #if str( $options_type.bgfile_type.bgfile_type_selector ) == 'motif_file':
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
15 --bgfile --motif--
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
16 #elif str( $options_type.bgfile_type.bgfile_type_selector ) == 'bgfile':
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
17 --bgfile $options_type.bgfile_type.bgfile
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
18 #elif str( $options_type.bgfile_type.bgfile_type_selector ) == 'uniform_distr':
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
19 --bgfile --uniform--
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
20 #end if
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
21 $options_type.max_strand
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
22 --max-stored-scores $options_type.max_stored_scores
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
23
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
24 #if str( $options_type.motifs_cond.motif_selector) == 'yes':
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
25 #for $motif in $options_type.motifs_cond.motifs:
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
26 --motif $motif.motif
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
27 #end for
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
28 #end if
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
29
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
30 --motif-pseudo $options_type.motif_pseudo
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
31 $options_type.no_qvalue
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
32 $options_type.parse_genomic_coords
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
33
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
34 #if str( $options_type.psp_cond.psp_selector ) == 'yes':
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
35 --psp $options_type.psp_cond.input_psp
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
36 --alpha $options_type.psp_cond.alpha
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
37 #end if
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
38
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
39 #if str( $options_type.prior_dist_cond.prior_dist_selector ) == 'yes':
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
40 --prior-dist $options_type.prior_dist_cond.input_prior_dist
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
41 #end if
9
b69b8c6bbbde planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents: 7
diff changeset
42 #end if
12
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
43 '$input_motifs'
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
44 #if str($fasta_type.fasta_type_selector) == 'history':
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
45 '${fasta_type.input_database}'
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
46 #else:
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
47 '${fasta_type.input_database.fields.path}'
9
b69b8c6bbbde planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents: 7
diff changeset
48 #end if
12
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
49 && mv ./out/fimo.html '${html_outfile}'
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
50 && mv ./out/fimo.txt '${txt_outfile}'
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
51 && mv ./out/fimo.xml '${xml_outfile}'
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
52 && mv ./out/fimo.gff '${gff_outfile}'
9
b69b8c6bbbde planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents: 7
diff changeset
53 ]]></command>
0
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
54 <inputs>
12
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
55 <param name="input_motifs" type="data" format="memexml" label="DREME or MEME output XML file"
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
56 help="DREME or MEME output XML file containing found motifs"/>
0
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
57 <conditional name="fasta_type">
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
58 <param name="fasta_type_selector" type="select" label="Source for sequence to search">
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
59 <option value="cached">Locally Cached sequences</option>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
60 <option value="history" selected="true">Sequences from your history</option>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
61 </param>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
62 <when value="cached">
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
63 <param name="input_database" type="select" label="Genome to search">
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
64 <options from_data_table="all_fasta" />
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
65 </param>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
66 </when>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
67 <when value="history">
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
68 <param format="fasta" name="input_database" type="data" label="Sequences"/>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
69 </when>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
70 </conditional>
12
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
71 <param name="scanrc" label="Check reverse complement strand" type="boolean"
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
72 truevalue="" falsevalue="--norc" checked="False"
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
73 help="Search for motifs also on reverse complement strand"/>
0
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
74 <conditional name="options_type">
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
75 <param name="options_type_selector" type="select" label="Options configuration">
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
76 <option value="basic" selected="true">Basic</option>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
77 <option value="advanced">Advanced</option>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
78 </param>
12
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
79 <when value="basic"/>
0
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
80 <when value="advanced">
12
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
81 <param name="thresh" type="float" value="1e-4" argument="--thresh"
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
82 label="Output threshold for displaying search results"
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
83 help="Only output results with a p-value less than the given threshold. To apply set threshold to q-values rather than p-values, set --qv-thresh."/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
84 <param name="qv_thresh" label="Apply output threshold to q-values?" argument="--qv-thresh"
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
85 type="boolean" truevalue="--qv_thresh" falsevalue="" checked="False"
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
86 help="Default: apply set threshold on p-values"/>
0
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
87 <conditional name="bgfile_type">
12
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
88 <param name="bgfile_type_selector" type="select" label="Background model selection">
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
89 <option value="default" selected="true">Use embedded letter frequencies from non-redundant DNA/protein database</option>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
90 <option value="motif_file">Use 0-order letter frequencies from motif file</option>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
91 <option value="bgfile">Use 0-order letter frequencies from background file</option>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
92 <option value="uniform_distr">Use uniform letter frequencies</option>
0
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
93 </param>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
94 <when value="motif_file" />
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
95 <when value="default" />
12
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
96 <when value="uniform_distr" />
0
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
97 <when value="bgfile">
12
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
98 <param name="bgfile" type="data" format="txt" optional="True" label="Background model file" help="File must be in Markov background model format (see MEME suite tool fasta-get-markov for details)"/>
0
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
99 </when>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
100 </conditional>
12
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
101 <param name="max_strand" label="Report best match in case of overlapping matches on both strands?" argument="--max-strand"
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
102 type="boolean" truevalue="--max-strand" falsevalue="" checked="False"
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
103 help="If matches on both strands at a given position satisfy the output threshold, only report the match for the strand with the higher score. If the scores are tied, the matching strand is chosen at random (default: report both matches)."/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
104 <param name="max_stored_scores" type="integer" value="100000" argument="--max-stored-scores"
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
105 label="Maximum number of scores that will be stored"
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
106 help="Keeping a complete list of scores may exceed available memory. Once the number of stored scores reaches the maximum allowed, the least significant 50% of scores will be dropped. In this case, the list of reported motifs may be incomplete and the q-value calculation will be approximate."/>
0
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
107 <conditional name="motifs_cond">
12
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
108 <param name="motif_selector" type="select" label="Specify single input motifs for scanning?">
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
109 <option value="no" selected="true">No</option>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
110 <option value="yes">Yes</option>
0
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
111 </param>
12
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
112 <when value="no"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
113 <when value="yes">
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
114 <repeat name="motifs" title="Supply input motif ID">
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
115 <param name="motif" type="text" value="" label="Motif ID" />
0
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
116 </repeat>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
117 </when>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
118 </conditional>
12
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
119 <param name="motif_pseudo" type="float" value="0.1" argument="--motif-pseudo"
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
120 label="Pseudocount to add to counts in motif matrix"
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
121 help="A pseudocount to be added to each count in the motif matrix, after first multiplying by the corresponding background frequency"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
122 <param name="no_qvalue" label="Disable q-value calculation?"
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
123 type="boolean" truevalue="--no-qvalue" falsevalue="" checked="False" argument="--no-qvalue"
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
124 help="The q-value calculation is that of Benjamini and Hochberg (1995) (default: calculate q-value for each p-value)"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
125 <param name="parse_genomic_coords" label="Check each sequence header for UCSC-style genomic coordinates?"
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
126 type="boolean" truevalue="--parse-genomic-coord" falsevalue="" checked="False" argument="--parse-genomic-coord"
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
127 help=" If genomic coordinates are found they will be used as the coordinates in the output."/>
0
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
128 <conditional name="psp_cond">
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
129 <param name="psp_selector" type="select" label="Use position-specific priors?">
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
130 <option value="no" selected="true">No</option>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
131 <option value="yes">Yes</option>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
132 </param>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
133 <when value="no"/>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
134 <when value="yes">
12
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
135 <param name="input_psp" type="data" format="txt" argument="--psp"
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
136 label="Select file containing position-specific priors"
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
137 help="File should be in MEME PSP format or wiggle format (can be generated by MEME suite tool create-priors)"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
138 <param name="alpha" type="float" value="1.0" min="0" max="1.0" argument="--alpha"
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
139 label="Alpha parameter for calculating position-specific priors"
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
140 help="Represents the fraction of all transcription factor binding sites that are binding sites for the TF of interest (must be between 0 and 1)"/>
0
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
141 </when>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
142 </conditional>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
143 <conditional name="prior_dist_cond">
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
144 <param name="prior_dist_selector" type="select" label="Use binned distribution of priors?">
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
145 <option value="no" selected="true">No</option>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
146 <option value="yes">Yes</option>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
147 </param>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
148 <when value="no"/>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
149 <when value="yes">
12
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
150 <param name="input_prior_dist" type="data" format="txt" argument="--prior-dist"
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
151 label="Select dataset containing binned distribution of priors"
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
152 help="This file can be generated using the MEME suite tool create-priors"/>
0
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
153 </when>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
154 </conditional>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
155 </when>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
156 </conditional>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
157 <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False">
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
158 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
159 </param>
12
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
160 <section name="output_options" title="Additional output options">
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
161 <param name="html_outfile" type="boolean" value="False" label="Output HTML file" help="FIMO HTML output file"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
162 <param name="xml_outfile" type="boolean" value="False" label="Output XML file" help="FIMO XML output file"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
163 <param name="gff_outfile" type="boolean" value="False" label="Output GFF file" help="FIMO GFF output file"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
164 </section>
0
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
165 </inputs>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
166 <outputs>
12
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
167 <data format="txt" name="txt_outfile" label="${tool.name} on ${on_string} (text)">
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
168 <actions>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
169 <conditional name="fasta_type.fasta_type_selector">
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
170 <when value="cached">
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
171 <action type="metadata" name="dbkey">
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
172 <option type="from_data_table" name="all_fasta" column="1" offset="0">
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
173 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
174 </option>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
175 </action>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
176 </when>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
177 </conditional>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
178 </actions>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
179 </data>
0
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
180 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)">
12
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
181 <filter>(output_options['html_outfile'] is True)</filter>
0
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
182 <actions>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
183 <conditional name="fasta_type.fasta_type_selector">
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
184 <when value="cached">
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
185 <action type="metadata" name="dbkey">
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
186 <option type="from_data_table" name="all_fasta" column="1" offset="0">
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
187 <filter type="param_value" column="0" value="seq" keep="True"/>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
188 <filter type="param_value" ref="fasta_type.input_database" column="1"/>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
189 </option>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
190 </action>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
191 </when>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
192 </conditional>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
193 </actions>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
194 </data>
12
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
195 <data format="txt" name="gff_outfile" label="${tool.name} on ${on_string} (gff)">
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
196 <filter>(output_options['gff_outfile'] is True)</filter>
0
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
197 <actions>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
198 <conditional name="fasta_type.fasta_type_selector">
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
199 <when value="cached">
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
200 <action type="metadata" name="dbkey">
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
201 <option type="from_data_table" name="all_fasta" column="1" offset="0">
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
202 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
203 </option>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
204 </action>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
205 </when>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
206 </conditional>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
207 </actions>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
208 </data>
12
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
209 <data format="memexml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)">
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
210 <filter>(output_options['xml_outfile'] is True)</filter>
0
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
211 <actions>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
212 <conditional name="fasta_type.fasta_type_selector">
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
213 <when value="cached">
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
214 <action type="metadata" name="dbkey">
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
215 <option type="from_data_table" name="all_fasta" column="1" offset="0">
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
216 <filter type="param_value" ref="fasta_type.input_database" column="0"/>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
217 </option>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
218 </action>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
219 </when>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
220 </conditional>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
221 </actions>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
222 </data>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
223 </outputs>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
224 <tests>
12
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
225 <test expect_num_outputs="4">
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
226 <param name="input_motifs" value="meme_fimo_input_1.xml" ftype="memexml"/>
0
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
227 <param name="fasta_type_selector" value="history"/>
12
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
228 <param name="input_database" value="hsa_chrM.fa" ftype="fasta"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
229 <param name="scanrc" value="true"/>
0
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
230 <param name="options_type_selector" value="basic"/>
12
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
231 <param name="html_outfile" value="True"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
232 <param name="xml_outfile" value="True"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
233 <param name="gff_outfile" value="True"/>
0
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
234 <param name="non_commercial_use" value="True"/>
12
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
235 <output name="html_outfile" file="fimo_output_test1.html" lines_diff="20"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
236 <output name="txt_outfile" file="fimo_output_test1.txt"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
237 <output name="xml_outfile" file="fimo_output_test1.xml" lines_diff="20"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
238 <output name="gff_outfile" file="fimo_output_test1.gff"/>
2
8d8905e040cf Uploaded
iuc
parents: 1
diff changeset
239 </test>
12
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
240 <test expect_num_outputs="4">
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
241 <param name="input_motifs" value="dreme_fimo_input_1.xml" ftype="memexml"/>
2
8d8905e040cf Uploaded
iuc
parents: 1
diff changeset
242 <param name="fasta_type_selector" value="history"/>
12
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
243 <param name="input_database" value="hsa_chrM.fa" ftype="fasta"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
244 <param name="scanrc" value="true"/>
2
8d8905e040cf Uploaded
iuc
parents: 1
diff changeset
245 <param name="options_type_selector" value="advanced"/>
12
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
246 <param name="bgfile_type_selector" value="bgfile"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
247 <param name="bgfile" value="fimo_background_probs_hsa_chrM.txt"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
248 <param name="html_outfile" value="True"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
249 <param name="xml_outfile" value="True"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
250 <param name="gff_outfile" value="True"/>
2
8d8905e040cf Uploaded
iuc
parents: 1
diff changeset
251 <param name="non_commercial_use" value="True"/>
12
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
252 <output name="html_outfile" file="fimo_output_test2.html" lines_diff="20"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
253 <output name="txt_outfile" file="fimo_output_test2.txt"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
254 <output name="xml_outfile" file="fimo_output_test2.xml" lines_diff="20"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
255 <output name="gff_outfile" file="fimo_output_test2.gff"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
256 </test>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
257 <test expect_num_outputs="3">
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
258 <param name="input_motifs" value="dreme_fimo_input_1.xml" ftype="memexml"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
259 <param name="fasta_type_selector" value="history"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
260 <param name="input_database" value="hsa_chrM.fa" ftype="fasta"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
261 <param name="scanrc" value="true"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
262 <param name="options_type_selector" value="advanced"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
263 <param name="thresh" value="0.01"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
264 <param name="bgfile_type_selector" value="uniform_distr"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
265 <param name="motif_selector" value="yes"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
266 <repeat name="motifs">
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
267 <param name="motif" value="ACTAAYH"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
268 </repeat>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
269 <param name="html_outfile" value="True"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
270 <param name="xml_outfile" value="True"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
271 <param name="gff_outfile" value="False"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
272 <param name="non_commercial_use" value="True"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
273 <output name="html_outfile" file="fimo_output_test3.html" lines_diff="20"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
274 <output name="txt_outfile" file="fimo_output_test3.txt"/>
e37874b1f811 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 10
diff changeset
275 <output name="xml_outfile" file="fimo_output_test3.xml" lines_diff="20"/>
0
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
276 </test>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
277 </tests>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
278 <help>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
279
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
280 .. class:: warningmark
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
281
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
282 **WARNING: This tool is only available for non-commercial use. Use for educational, research and non-profit purposes is permitted.
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
283 Before using, be sure to review, agree, and comply with the license.**
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
284
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
285 FIMO scans a sequence database for individual matches to each of the motifs you provide (sample output for motifs and sequences).
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
286 The name FIMO stands for 'Find Individual Motif Occurrences'. The program searches a database of sequences for occurrences of
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
287 known motifs, treating each motif independently. Motifs must be in MEME Motif Format. You can define the statistical threshold
2
8d8905e040cf Uploaded
iuc
parents: 1
diff changeset
288 (p-value) for motifs and whether FIMO scans just the given sequences or their reverse complements (where applicable).
0
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
289
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
290 .. class:: infomark
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
291
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
292 For detailed information on FIMO, click here_, or view the license_.
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
293
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
294 .. _here: http://meme-suite.org/doc/fimo.html?man_type=web
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
295 .. _license: http://meme-suite.org/doc/copyright.html?man_type=web
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
296
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
297 </help>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
298 <citations>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
299 <citation type="doi">10.1093/bioinformatics/btr064</citation>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
300 </citations>
27c742760a84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff changeset
301 </tool>