Mercurial > repos > iuc > meme_meme
comparison meme.xml @ 9:794b2859c286 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
author | iuc |
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date | Thu, 29 Jun 2017 20:39:45 -0400 |
parents | 487ce3fa1822 |
children | b8c05adb68da |
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8:e8b209806a20 | 9:794b2859c286 |
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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> |