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comparison meme.xml @ 6:3215af722a0a 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 20:39:17 -0400
parents 6c731d47c3be
children e2b2f2394afb
comparison
equal deleted inserted replaced
5:70b56282c7dc 6:3215af722a0a
1 <tool id="meme_meme" name="MEME" version="4.11.1.0"> 1 <tool id="meme_meme" name="MEME" version="4.11.2.0">
2 <description>- Multiple Em for Motif Elicitation</description> 2 <description>- Multiple Em for Motif Elicitation</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 meme '$input1'
9 <exit_code range="1:" /> 9 -o '${html_outfile.files_path}'
10 <!-- In case the return code has not been set propery check stderr too --> 10 -nostatus
11 <regex match="Error:" /> 11 -maxsize 1000000
12 <regex match="Exception:" /> 12 #if str( $options_type.options_type_selector ) == 'advanced':
13 </stdio> 13 -sf '${ str( $options_type.sf ).replace( " ", "_" ) }'
14 <command> 14 -${options_type.alphabet_type.alphabet_type_selector}
15 <![CDATA[ 15 -mod '${options_type.mod_type.mod_type_selector}'
16 meme "$input1" 16 -nmotifs '${options_type.nmotifs}'
17 -o "${html_outfile.files_path}" 17 -wnsites '${options_type.wnsites}'
18 -nostatus 18 #if $options_type.evt < float('inf'):
19 -maxsize 1000000 19 -evt '${options_type.evt}'
20 #if str( $options_type.options_type_selector ) == 'advanced': 20 #end if
21 -sf "${ str( $options_type.sf ).replace( ' ', '_' ) }" 21 #if str( $options_type.mod_type.mod_type_selector ) != 'oops':
22 -${options_type.alphabet_type.alphabet_type_selector} 22 #if str( $options_type.mod_type.motif_occurrence_type.motif_occurrence_type_selector ) == 'nsites':
23 -mod "${options_type.mod_type.mod_type_selector}" 23 -nsites '${options_type.mod_type.motif_occurrence_type.nsites}'
24 -nmotifs "${options_type.nmotifs}" 24 #elif str( $options_type.mod_type.motif_occurrence_type.motif_occurrence_type_selector ) == 'min_max_sites':
25 -wnsites "${options_type.wnsites}" 25 -minsites '${options_type.mod_type.motif_occurrence_type.minsites}'
26 #if $options_type.evt < float('inf'): 26 -maxsites '${options_type.mod_type.motif_occurrence_type.maxsites}'
27 -evt "${options_type.evt}" 27 #end if
28 #end if 28 #end if
29 #if str( $options_type.mod_type.mod_type_selector ) != 'oops': 29 #if str( $options_type.motif_width_type.motif_width_type_selector ) == 'exact':
30 #if str( $options_type.mod_type.motif_occurrence_type.motif_occurrence_type_selector ) == 'nsites': 30 -w '${options_type.motif_width_type.width}'
31 -nsites "${options_type.mod_type.motif_occurrence_type.nsites}" 31 #else
32 #elif str( $options_type.mod_type.motif_occurrence_type.motif_occurrence_type_selector ) == 'min_max_sites': 32 -minw '${options_type.motif_width_type.minw}'
33 -minsites "${options_type.mod_type.motif_occurrence_type.minsites}" 33 -maxw '${options_type.motif_width_type.maxw}'
34 -maxsites "${options_type.mod_type.motif_occurrence_type.maxsites}" 34 #end if
35 #end if 35 #if str( $options_type.motif_trim_type.motif_trim_type_selector ) == 'nomatrim':
36 #end if 36 -nomatrim
37 #if str( $options_type.motif_width_type.motif_width_type_selector ) == 'exact': 37 #else
38 -w "${options_type.motif_width_type.width}" 38 -wg '${options_type.motif_trim_type.wg}'
39 #else 39 -ws '${options_type.motif_trim_type.ws}'
40 -minw "${options_type.motif_width_type.minw}" 40 ${options_type.motif_trim_type.noendgaps}
41 -maxw "${options_type.motif_width_type.maxw}" 41 #end if
42 #end if 42 #if str( $options_type.bfile ) != 'None':
43 #if str( $options_type.motif_trim_type.motif_trim_type_selector ) == 'nomatrim': 43 -bfile '${options_type.bfile}'
44 -nomatrim 44 #end if
45 #else 45 #if str( $options_type.pspfile ) != 'None':
46 -wg "${options_type.motif_trim_type.wg}" 46 -psp '${options_type.pspfile}'
47 -ws "${options_type.motif_trim_type.ws}" 47 #end if
48 ${options_type.motif_trim_type.noendgaps} 48 #if str( $options_type.alphabet_type.alphabet_type_selector ) == 'dna':
49 #end if 49 ${options_type.alphabet_type.revcomp} ${options_type.alphabet_type.pal}
50 #if str( $options_type.bfile ) != 'None': 50 #end if
51 -bfile "${options_type.bfile}" 51 -maxiter '${options_type.maxiter}'
52 #end if 52 -distance '${options_type.distance}'
53 #if str( $options_type.pspfile ) != 'None': 53 -prior '${options_type.alphabet_type.prior_type.prior_type_selector}'
54 -psp "${options_type.pspfile}" 54 #if str( $options_type.alphabet_type.prior_type.prior_type_selector ) != 'addone':
55 #end if 55 -b '${options_type.alphabet_type.prior_type.prior_b}'
56 #if str( $options_type.alphabet_type.alphabet_type_selector ) == "dna": 56 #if str( $options_type.alphabet_type.prior_type.plib ) != 'None':
57 ${options_type.alphabet_type.revcomp} ${options_type.alphabet_type.pal} 57 -plib '${options_type.alphabet_type.prior_type.plib}'
58 #end if 58 #end if
59 -maxiter "${options_type.maxiter}" 59 #end if
60 -distance "${options_type.distance}" 60 #if str( $options_type.alphabet_type.spmap_type.spmap_type_selector ) == 'cons':
61 -prior "${options_type.alphabet_type.prior_type.prior_type_selector}" 61 -cons '${options_type.alphabet_type.spmap_type.cons}'
62 #if str( $options_type.alphabet_type.prior_type.prior_type_selector ) != 'addone': 62 #else
63 -b "${options_type.alphabet_type.prior_type.prior_b}" 63 -spmap '${options_type.alphabet_type.spmap_type.spmap_type_selector}'
64 #if str( $options_type.alphabet_type.prior_type.plib ) != 'None': 64 -spfuzz '${options_type.alphabet_type.spmap_type.spfuzz}'
65 -plib "${options_type.alphabet_type.prior_type.plib}" 65 #end if
66 #end if 66 #if str( $options_type.branching_type.branching_type_selector ) == 'x_branch':
67 #end if 67 -x_branch
68 #if str( $options_type.alphabet_type.spmap_type.spmap_type_selector ) == 'cons': 68 -bfactor '${options_type.branching_type.bfactor}'
69 -cons "${options_type.alphabet_type.spmap_type.cons}" 69 -heapsize '${options_type.branching_type.heapsize}'
70 #else 70 #end if
71 -spmap "${options_type.alphabet_type.spmap_type.spmap_type_selector}" 71 #end if
72 -spfuzz "${options_type.alphabet_type.spmap_type.spfuzz}" 72 && mv '${html_outfile.files_path}/meme.html' '${html_outfile}'
73 #end if 73 && mv '${html_outfile.files_path}/meme.txt' '${txt_outfile}'
74 #if str( $options_type.branching_type.branching_type_selector ) == 'x_branch': 74 && mv '${html_outfile.files_path}/meme.xml' '${xml_outfile}'
75 -x_branch 75 ]]></command>
76 -bfactor "${options_type.branching_type.bfactor}"
77 -heapsize "${options_type.branching_type.heapsize}"
78 #end if
79 #end if
80 && mv ${html_outfile.files_path}/meme.html ${html_outfile}
81 && mv ${html_outfile.files_path}/meme.txt ${txt_outfile}
82 && mv ${html_outfile.files_path}/meme.xml ${xml_outfile}
83 ]]>
84 </command>
85 <inputs> 76 <inputs>
86 <param format="fasta" name="input1" type="data" label="Sequences"/> 77 <param format="fasta" name="input1" type="data" label="Sequences"/>
87 <conditional name="options_type"> 78 <conditional name="options_type">
88 <param name="options_type_selector" type="select" label="Options Configuration"> 79 <param name="options_type_selector" type="select" label="Options Configuration">
89 <option value="basic" selected="true">Basic</option> 80 <option value="basic" selected="true">Basic</option>