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comparison misp.xml @ 0:87f7630ab82f draft default tip

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author jjohnson
date Thu, 25 Sep 2014 14:05:16 -0400
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1 <tool name="MISP: Motif-based Interval Screener with PSSM" id="misp" version="0.1.0">
2 <description>Input one or more motifs, find all hits in peak regions</description>
3 <requirements>
4 <requirement type="package" version="2013-11-28">misp</requirement>
5 <requirement type="package" version="2.19.1">bedtools</requirement>
6 </requirements>
7 <command>
8 #if $motifopt.motifopt_select == "upload"
9 #set $motif_db = str($motifopt.motif_file)
10 #else
11 #set $motif_db = "\${MISP_DATABASE_PATH}/motif/cistrome.db"
12 #end if
13 #set $motif_id = str($motifopt.motif_id)
14 #if $refGenomeSource.genomeSource == "history":
15 #set $genome_file = $refGenomeSource.ownFile
16 #else:
17 #set $genome_file = $refGenomeSource.index.fields.path
18 #end if
19 bedtools getfasta -fi $genome_file -bed $bedfile -fo out.fasta > /dev/null &amp;&amp;
20 misp out.fasta $motif_db $pvalue $motif_id output &amp;> $log &amp;&amp;
21 cat output* > $outputtxt
22 </command>
23 <stdio>
24 <exit_code range="1:" level="fatal" description="Error" />
25 </stdio>
26 <inputs>
27 <param format="bed" name="bedfile" type="data" label="bed file for regions">
28 <validator type="unspecified_build" />
29 </param>
30 <conditional name="refGenomeSource">
31 <param name="genomeSource" type="select" label="Use a built in reference genome or own from your history" help="Built-ins genomes were created using default options">
32 <option value="cached" selected="True">Use a built-in genome</option>
33 <option value="history">Use a genome from history</option>
34 </param>
35 <when value="cached">
36 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
37 <options from_data_table="all_fasta">
38 <filter type="data_meta" ref="bedfile" key="dbkey" column="1" multiple="True" separator="," />
39 <validator type="no_options" message="No reference build available for selected input" />
40 </options>
41 </param>
42 </when>
43 <when value="history">
44 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
45 </when> <!-- history -->
46 </conditional> <!-- refGenomeSource -->
47 <conditional name="motifopt">
48 <param name="motifopt_select" type="select" label="upload a motif or select from our database.">
49 <option value="upload">Use uploaded motif</option>
50 <option value="database">Use motif in cistrome database.</option>
51 </param>
52 <when value="upload">
53 <param name="motif_file" type="data" label="motif file" />
54 <param name="motif_id" type="text" label="The motif id in uploaded motif file. Or write 'all' to run all motifs in the file." />
55 </when>
56 <when value="database">
57 <param name="motif_id" type="text" label="The motif id in Cistrome motif collection. Or write 'all' to run all motifs in the file." />
58 </when>
59 </conditional>
60 <param name="pvalue" type="float" label="p-value cutoff for the motif screen" value="0.001">
61 <validator type="in_range" max="1" min="0" message="pvalue is out of range, width has to be between 0 to 1" />
62 </param>
63 </inputs>
64 <outputs>
65 <data format="txt" name="outputtxt" label="MISP hits on ${bedfile.name}"/>
66 <data format="txt" name="log" label="Log of MISP on ${bedfile.name}"/>
67 </outputs>
68 <tests>
69 <test>
70 <param name="bedfile" type="bed" value="test.bed" dbkey="mm9"/>
71 <param name="genomeSource" value="history" />
72 <param name="ownFile" type="fasta" value="mm9_chr19_part.fasta" dbkey="mm9"/>
73 <param name="motifopt_select" value="upload" />
74 <param name="motif_file" value="misp_motif" />
75 <param name="motif_id" value="M00139" />
76 <param name="pvalue" value="0.001" />
77 <output name="outputtxt" file="misp.hits"/>
78 <output name="log" file="misp.log"/>
79 </test>
80 </tests>
81 <help>
82 Given a motif, this tool will find all hits of the motif in specified region.
83
84 -----
85
86 **Formula**
87
88 .. image:: ./static/cistrome_icons/misp_formula.png
89
90 -----
91
92 **TIP:** The source code of misp is available at bitbucket_
93
94 .. _bitbucket: https://bitbucket.org/hanfeisun/misp/overview
95
96
97 **TIP:** To check the motif id in our database, click here_
98
99 .. _here: http://cistrome.org/motif/
100
101 -----
102
103 Left to right shoule be:
104
105 T
106
107 C
108
109 G
110
111 A
112
113 **Example of the format of uploaded motif database.**
114
115 M00139
116
117 0.667 0.111 0.667 0.01 0.01 0.01 0.01 0.01 0.333 0.01 0.01 0.333 0.444 0.222 0.01 0.01 0.01 0.01
118
119 0.01 0.546 0.111 0.97 0.01 0.97 0.01 0.97 0.111 0.01 0.444 0.444 0.536 0.333 0.222 0.111 0.01 0.222
120
121 0.01 0.333 0.111 0.01 0.01 0.01 0.97 0.01 0.222 0.01 0.536 0.111 0.01 0.333 0.758 0.556 0.667 0.667
122
123 0.313 0.01 0.111 0.01 0.97 0.01 0.01 0.01 0.334 0.97 0.01 0.112 0.01 0.112 0.01 0.323 0.313 0.101
124
125 hPDI060
126
127 0.01 0.01 0.01 0.625 0.01 0.01
128
129 0.97 0.97 0.97 0.01 0.5 0.97
130
131 0.01 0.01 0.01 0.01 0.48 0.01
132
133 0.01 0.01 0.01 0.355 0.01 0.01
134 </help>
135
136 </tool>