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comparison SMART/galaxy/mapperAnalyzer.xml @ 38:2c0c0a89fad7

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author m-zytnicki
date Thu, 02 May 2013 09:56:47 -0400
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37:d22fadc825e3 38:2c0c0a89fad7
1 <tool id="mapperAnalyzer" name="mapper analyzer">
2 <description>Read the output of an aligner, print statistics and possibly translate into GFF, BED or GBrowse formats. </description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
6 <command interpreter="python">
7 ../Java/Python/mapperAnalyzer.py -i $formatType.inputFileName1
8 #if $formatType.FormatInputFileName1 == 'bed':
9 -f bed
10 #elif $formatType.FormatInputFileName1 == 'gff3':
11 -f gff3
12 #elif $formatType.FormatInputFileName1 == 'sam':
13 -f sam
14 #elif $formatType.FormatInputFileName1 == 'bam':
15 -f bam
16 #elif $formatType.FormatInputFileName1 == 'seqmap':
17 -f seqmap
18 #end if
19
20 -q $formatType2.inputFileName2
21 #if $formatType2.FormatInputFileName2 == 'fasta':
22 -k fasta
23 #elif $formatType2.FormatInputFileName2 == 'fastq':
24 -k fastq
25 #end if
26
27
28 #if $optionnumber.number == 'Yes':
29 -n $optionnumber.numberVal
30 #end if
31 #if $optionsize.size == 'Yes':
32 -s $optionsize.sizeVal
33 #end if
34 #if $optionidentity.identity == 'Yes':
35 -d $optionidentity.identityVal
36 #end if
37 #if $optionmismatch.mismatch == 'Yes':
38 -m $optionmismatch.mismatchVal
39 #end if
40 #if $optiongap.gap == 'Yes':
41 -p $optiongap.gapVal
42 #end if
43 #if $optiontitle.title == 'Yes':
44 -t $optiontitle.titleVal
45 #end if
46 #if $optionappend.append == 'Yes':
47 -a $optionappend.appendfile
48 #end if
49
50 $merge
51 $remove
52 $remain
53 -o $outputFileGFF
54 </command>
55
56 <inputs>
57 <conditional name="formatType">
58 <param name="FormatInputFileName1" type="select" label="Input File mapping Format">
59 <option value="bed">bed</option>
60 <option value="gff3">gff3</option>
61 <option value="sam">sam</option>
62 <option value="bam">bam</option>
63 <option value="seqmap" selected="true">seqmap</option>
64 </param>
65 <when value="bed">
66 <param name="inputFileName1" format="bed" type="data" label="Input File"/>
67 </when>
68 <when value="gff3">
69 <param name="inputFileName1" format="gff3" type="data" label="Input File"/>
70 </when>
71 <when value="sam">
72 <param name="inputFileName1" format="sam" type="data" label="Input File"/>
73 </when>
74 <when value="bam">
75 <param name="inputFileName1" format="bam" type="data" label="Input File"/>
76 </when>
77 <when value="seqmap">
78 <param name="inputFileName1" format="seqmap" type="data" label="Input File"/>
79 </when>
80 </conditional>
81
82 <conditional name="formatType2">
83 <param name="FormatInputFileName2" type="select" label="Reference sequence File Format">
84 <option value="fasta" selected="true">fasta</option>
85 <option value="fastq">fastq</option>
86 </param>
87 <when value="fasta">
88 <param name="inputFileName2" format="fasta" type="data" label="Reference sequence File Format"/>
89 </when>
90 <when value="fastq">
91 <param name="inputFileName2" format="fastq" type="data" label="Reference sequence File Format"/>
92 </when>
93 </conditional>
94
95 <conditional name="optionnumber">
96 <param name="number" type="select" label="max. number of occurrences of a sequence">
97 <option value="Yes">Yes</option>
98 <option value="No" selected="true">No</option>
99 </param>
100 <when value="Yes">
101 <param name="numberVal" type="integer" value="0"/>
102 </when>
103 <when value="No">
104 </when>
105 </conditional>
106
107 <conditional name="optionsize">
108 <param name="size" type="select" label="minimum pourcentage of size ">
109 <option value="Yes">Yes</option>
110 <option value="No" selected="true">No</option>
111 </param>
112 <when value="Yes">
113 <param name="sizeVal" type="integer" value="0"/>
114 </when>
115 <when value="No">
116 </when>
117 </conditional>
118
119 <conditional name="optionidentity">
120 <param name="identity" type="select" label="minimum pourcentage of identity ">
121 <option value="Yes">Yes</option>
122 <option value="No" selected="true">No</option>
123 </param>
124 <when value="Yes">
125 <param name="identityVal" type="integer" value="0"/>
126 </when>
127 <when value="No">
128 </when>
129 </conditional>
130
131 <conditional name="optionmismatch">
132 <param name="mismatch" type="select" label="maximum number of mismatches">
133 <option value="Yes">Yes</option>
134 <option value="No" selected="true">No</option>
135 </param>
136 <when value="Yes">
137 <param name="mismatchVal" type="integer" value="0"/>
138 </when>
139 <when value="No">
140 </when>
141 </conditional>
142
143 <conditional name="optiongap">
144 <param name="gap" type="select" label="maximum number of gaps">
145 <option value="Yes">Yes</option>
146 <option value="No" selected="true">No</option>
147 </param>
148 <when value="Yes">
149 <param name="gapVal" type="integer" value="0"/>
150 </when>
151 <when value="No">
152 </when>
153 </conditional>
154
155 <conditional name="optiontitle">
156 <param name="title" type="select" label="title of the plots ">
157 <option value="Yes">Yes</option>
158 <option value="No" selected="true">No</option>
159 </param>
160 <when value="Yes">
161 <param name="titleVal" type="text" value="title of the UCSC track" />
162 </when>
163 <when value="No">
164 </when>
165 </conditional>
166
167 <conditional name="optionappend">
168 <param name="append" type="select" label="append to GFF3 file">
169 <option value="Yes">Yes</option>
170 <option value="No" selected="true">No</option>
171 </param>
172 <when value="Yes">
173 <param name="appendfile" type="data" format="gff3" label="append a file"/>
174 </when>
175 <when value="No">
176 </when>
177 </conditional>
178
179 <param name="merge" type="boolean" truevalue="-e" falsevalue="" checked="false" label="merge exons when introns are short "/>
180 <param name="remove" type="boolean" truevalue="-x" falsevalue="" checked="false" label="remove transcripts when exons are short"/>
181 <param name="remain" type="boolean" truevalue="-r" falsevalue="" checked="false" label="print the unmatched sequences "/>
182 </inputs>
183
184 <outputs>
185 <data name="outputFileGFF" format="gff3" label="[mapper analyzer] output file"/>
186 </outputs>
187
188 <help>
189 Maybe the first program you may use. It reads a set of mapping given by the tool you have used to map your data on the reference genome and translate it to a set of genomic coordinates. You also have the possibility to extract only those that you are interested in (few matches in the genome, few errors in the mapping, etc.). You can also select those reads which map less than a given of times in the genome. Moreover, you can output the data in various different formats, which you can use to visualize them *via* UCSC genome browser or GBrowse. Unmatched reads can be written in an other file, in case you would like to try to map them with another tool (may sometimes work!).
190
191 You can filter your data according to:
192
193 - number of errors in the mapping
194
195 - number of occurrences of the mapping in the genome
196
197 - size of the read mapped
198
199 - number of gaps in the mapping
200
201 The script needs an input file (your mapped reads) together with its format and the read sequences file together with its format (FASTA or FASTQ). If you want, you can also append the results of this script to another GFF3 file. This is useful when the GFF3 file is the result of the mapping using another tool.
202
203 By default, any gap in the alignment to the reference sequence is treated like an exon. You can decide to remove this feature by merging short introns (actually, gaps).
204 </help>
205 </tool>