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comparison smart_toolShed/SMART/galaxy/mapperAnalyzer.xml @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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-1:000000000000 0:e0f8dcca02ed
1 <tool id="mapperAnalyzer" name="mapper analyzer">
2 <description>Read the output of an aligner, print statistics and possibly translate into BED or GBrowse formats. </description>
3 <command interpreter="python">
4 ../Java/Python/mapperAnalyzer.py -i $formatType.inputFileName1
5 #if $formatType.FormatInputFileName1 == 'bed':
6 -f bed
7 #elif $formatType.FormatInputFileName1 == 'gff3':
8 -f gff3
9 #elif $formatType.FormatInputFileName1 == 'sam':
10 -f sam
11 #elif $formatType.FormatInputFileName1 == 'bam':
12 -f bam
13 #elif $formatType.FormatInputFileName1 == 'seqmap':
14 -f seqmap
15 #end if
16
17 -q $formatType2.inputFileName2
18 #if $formatType2.FormatInputFileName2 == 'fasta':
19 -k fasta
20 #elif $formatType2.FormatInputFileName2 == 'fastq':
21 -k fastq
22 #end if
23
24
25 #if $optionnumber.number == 'Yes':
26 -n $optionnumber.numberVal
27 #end if
28 #if $optionsize.size == 'Yes':
29 -s $optionsize.sizeVal
30 #end if
31 #if $optionidentity.identity == 'Yes':
32 -d $optionidentity.identityVal
33 #end if
34 #if $optionmismatch.mismatch == 'Yes':
35 -m $optionmismatch.mismatchVal
36 #end if
37 #if $optiongap.gap == 'Yes':
38 -p $optiongap.gapVal
39 #end if
40 #if $optiontitle.title == 'Yes':
41 -t $optiontitle.titleVal
42 #end if
43 #if $optionappend.append == 'Yes':
44 -a $optionappend.appendfile
45 #end if
46
47 $merge
48 $remove
49 $remain
50 -o $outputFileGFF
51 </command>
52
53 <inputs>
54 <conditional name="formatType">
55 <param name="FormatInputFileName1" type="select" label="Input File mapping Format">
56 <option value="bed">bed</option>
57 <option value="gff3">gff3</option>
58 <option value="sam">sam</option>
59 <option value="bam">bam</option>
60 <option value="seqmap" selected="true">seqmap</option>
61 </param>
62 <when value="bed">
63 <param name="inputFileName1" format="bed" type="data" label="Input File"/>
64 </when>
65 <when value="gff3">
66 <param name="inputFileName1" format="gff3" type="data" label="Input File"/>
67 </when>
68 <when value="sam">
69 <param name="inputFileName1" format="sam" type="data" label="Input File"/>
70 </when>
71 <when value="bam">
72 <param name="inputFileName1" format="bam" type="data" label="Input File"/>
73 </when>
74 <when value="seqmap">
75 <param name="inputFileName1" format="seqmap" type="data" label="Input File"/>
76 </when>
77 </conditional>
78
79 <conditional name="formatType2">
80 <param name="FormatInputFileName2" type="select" label="Reference sequence File Format">
81 <option value="fasta" selected="true">fasta</option>
82 <option value="fastq">fastq</option>
83 </param>
84 <when value="fasta">
85 <param name="inputFileName2" format="fasta" type="data" label="Reference sequence File Format"/>
86 </when>
87 <when value="fastq">
88 <param name="inputFileName2" format="fastq" type="data" label="Reference sequence File Format"/>
89 </when>
90 </conditional>
91
92
93 <conditional name="optionnumber">
94 <param name="number" type="select" label="max. number of occurrences of a sequence">
95 <option value="Yes">Yes</option>
96 <option value="No" selected="true">No</option>
97 </param>
98 <when value="Yes">
99 <param name="numberVal" type="integer" value="0"/>
100 </when>
101 <when value="No">
102 </when>
103 </conditional>
104
105 <conditional name="optionsize">
106 <param name="size" type="select" label="minimum pourcentage of size ">
107 <option value="Yes">Yes</option>
108 <option value="No" selected="true">No</option>
109 </param>
110 <when value="Yes">
111 <param name="sizeVal" type="integer" value="0"/>
112 </when>
113 <when value="No">
114 </when>
115 </conditional>
116
117 <conditional name="optionidentity">
118 <param name="identity" type="select" label="minimum pourcentage of identity ">
119 <option value="Yes">Yes</option>
120 <option value="No" selected="true">No</option>
121 </param>
122 <when value="Yes">
123 <param name="identityVal" type="integer" value="0"/>
124 </when>
125 <when value="No">
126 </when>
127 </conditional>
128
129 <conditional name="optionmismatch">
130 <param name="mismatch" type="select" label="maximum number of mismatches">
131 <option value="Yes">Yes</option>
132 <option value="No" selected="true">No</option>
133 </param>
134 <when value="Yes">
135 <param name="mismatchVal" type="integer" value="0"/>
136 </when>
137 <when value="No">
138 </when>
139 </conditional>
140
141 <conditional name="optiongap">
142 <param name="gap" type="select" label="maximum number of gaps">
143 <option value="Yes">Yes</option>
144 <option value="No" selected="true">No</option>
145 </param>
146 <when value="Yes">
147 <param name="gapVal" type="integer" value="0"/>
148 </when>
149 <when value="No">
150 </when>
151 </conditional>
152
153 <conditional name="optiontitle">
154 <param name="title" type="select" label="title of the plots ">
155 <option value="Yes">Yes</option>
156 <option value="No" selected="true">No</option>
157 </param>
158 <when value="Yes">
159 <param name="titleVal" type="text" value="title of the UCSC track" />
160 </when>
161 <when value="No">
162 </when>
163 </conditional>
164
165 <conditional name="optionappend">
166 <param name="append" type="select" label="append to GFF3 file">
167 <option value="Yes">Yes</option>
168 <option value="No" selected="true">No</option>
169 </param>
170 <when value="Yes">
171 <param name="appendfile" type="data" format="gff3" label="append a file"/>
172 </when>
173 <when value="No">
174 </when>
175 </conditional>
176
177 <param name="merge" type="boolean" truevalue="-e" falsevalue="" checked="false" label="merge exons when introns are short "/>
178 <param name="remove" type="boolean" truevalue="-x" falsevalue="" checked="false" label="remove transcripts when exons are short"/>
179 <param name="remain" type="boolean" truevalue="-r" falsevalue="" checked="false" label="print the unmatched sequences "/>
180 </inputs>
181
182 <outputs>
183 <data name="outputFileGFF" format="gff3" label="[mapperAnalyzer] out file"/>
184 </outputs>
185
186 </tool>