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comparison fimo.xml @ 9:b69b8c6bbbde draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
author iuc
date Thu, 29 Jun 2017 20:39:32 -0400
parents de3c73f58451
children ce2feec4c8d2
comparison
equal deleted inserted replaced
8:8a042b09be8e 9:b69b8c6bbbde
1 <tool id="meme_fimo" name="FIMO" version="4.11.1.0"> 1 <tool id="meme_fimo" name="FIMO" version="4.11.2.0">
2 <description>- Scan a set of sequences for motifs.</description> 2 <description>- Scan a set of sequences for motifs.</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="1.3.20">graphicsmagick</requirement> 4 <import>macros.xml</import>
5 <requirement type="package" version="4.11.1">meme</requirement> 5 </macros>
6 </requirements> 6 <expand macro="requirements" />
7 <stdio> 7 <command detect_errors="exit_code"><![CDATA[
8 <!-- Anything other than zero is an error --> 8 mkdir -p output &&
9 <exit_code range="1:" /> 9 python '$__tool_directory__/fimo_wrapper.py'
10 <!-- In case the return code has not been set propery check stderr too --> 10 --input_motifs '${input_motifs}'
11 <regex match="Error:" /> 11 #if str($fasta_type.fasta_type_selector) == 'history':
12 <regex match="Exception:" /> 12 --input_fasta '${fasta_type.input_database}'
13 </stdio> 13 #else:
14 <command> 14 --input_fasta '${fasta_type.input_database.fields.path}'
15 <![CDATA[ 15 #end if
16 mkdir -p output && 16 --options_type $options_type.options_type_selector
17 python $__tool_directory__/fimo_wrapper.py 17 #if str($options_type.options_type_selector) == 'advanced':
18 --input_motifs "${input_motifs}" 18 --alpha '${options_type.alpha}'
19 #if str($fasta_type.fasta_type_selector) == 'history': 19 #if str($options_type.bgfile_type.bgfile_type_selector) == 'motif_file':
20 --input_fasta "${fasta_type.input_database}" 20 --bgfile 'motif-file'
21 #else: 21 #elif str($options_type.bgfile_type.bgfile_type_selector) == 'bgfile':
22 --input_fasta "${fasta_type.input_database.fields.path}" 22 --bgfile '${options_type.bgfile_type.bgfile}'
23 #end if 23 #end if
24 --options_type $options_type.options_type_selector 24 ${options_type.max_strand}
25 #if str($options_type.options_type_selector) == 'advanced': 25 --max_stored_scores '${options_type.max_stored_scores}'
26 --alpha "${options_type.alpha}" 26 #if str($options_type.motifs_cond.motifs_selector) == 'no':
27 #if str($options_type.bgfile_type.bgfile_type_selector) == 'motif_file': 27 #for $motif in $options_type.motifs:
28 --bgfile "motif-file" 28 --motif '${motif.motif}'
29 #elif str($options_type.bgfile_type.bgfile_type_selector) == 'bgfile': 29 #end for
30 --bgfile "${options_type.bgfile_type.bgfile}" 30 #end if
31 #end if 31 --output_separate_motifs ${options_type.output_separate_motifs}
32 ${options_type.max_strand} 32 --motif_pseudo '${options_type.motif_pseudo}'
33 --max_stored_scores "${options_type.max_stored_scores}" 33 ${options_type.no_qvalue}
34 #if str($options_type.motifs_cond.motifs_selector) == 'no': 34 ${options_type.norc}
35 #for $motif in $options_type.motifs: 35 #if str($options_type.parse_genomic_coord_cond.parse_genomic_coord) == 'yes':
36 --motif "${motif.motif}" 36 --parse_genomic_coord 'yes'
37 #end for 37 --remove_duplicate_coords ${options_type.parse_genomic_coord_cond.remove_duplicate_coords}
38 #end if 38 #end if
39 --output_separate_motifs ${options_type.output_separate_motifs} 39 #if str($options_type.psp_cond.psp_selector) == 'yes':
40 --motif_pseudo "${options_type.motif_pseudo}" 40 --input_psp '${input_psp}'
41 ${options_type.no_qvalue} 41 #end if
42 ${options_type.norc} 42 #if str($options_type.prior_dist_cond.prior_dist_selector) == 'yes':
43 #if str($options_type.parse_genomic_coord_cond.parse_genomic_coord) == 'yes': 43 --input_prior_dist '${input_prior_dist}'
44 --parse_genomic_coord 'yes' 44 #end if
45 --remove_duplicate_coords ${options_type.parse_genomic_coord_cond.remove_duplicate_coords} 45 ${options_type.qv_thresh}
46 #end if 46 --thresh ${options_type.thresh}
47 #if str($options_type.psp_cond.psp_selector) == 'yes': 47 #end if
48 --input_psp "${input_psp}" 48 --output_path '${html_outfile.files_path}'
49 #end if 49 --html_output '${html_outfile}'
50 #if str($options_type.prior_dist_cond.prior_dist_selector) == 'yes': 50 --interval_output '${interval_outfile}'
51 --input_prior_dist "${input_prior_dist}" 51 --txt_output '${txt_outfile}'
52 #end if 52 --xml_output '${xml_outfile}'
53 ${options_type.qv_thresh} 53 --gff_output '${gff_outfile}'
54 --thresh ${options_type.thresh} 54 ]]></command>
55 #end if
56 --output_path '${html_outfile.files_path}'
57 --html_output "${html_outfile}"
58 --interval_output '${interval_outfile}'
59 --txt_output "${txt_outfile}"
60 --xml_output "${xml_outfile}"
61 --gff_output "${gff_outfile}"
62 ]]>
63 </command>
64 <inputs> 55 <inputs>
65 <param name="input_motifs" type="data" format="memexml" label="'MEME output' formatted file"/> 56 <param name="input_motifs" type="data" format="memexml" label="'MEME output' formatted file"/>
66 <conditional name="fasta_type"> 57 <conditional name="fasta_type">
67 <param name="fasta_type_selector" type="select" label="Source for sequence to search"> 58 <param name="fasta_type_selector" type="select" label="Source for sequence to search">
68 <option value="cached">Locally Cached sequences</option> 59 <option value="cached">Locally Cached sequences</option>