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comparison segemehl.xml @ 3:039547ad8fb8 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 21aaee40723b5341b4236edeb0e72995c2054053
author rnateam
date Fri, 16 Dec 2016 07:37:24 -0500
parents 0da425524259
children db367d012fa3
comparison
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2:0da425524259 3:039547ad8fb8
1 <tool id="segemehl" name="segemehl" version="0.1.6.0"> 1 <tool id="segemehl" name="segemehl" version="0.2.0">
2 <description>based short read aligner</description> 2 <description>based short read aligner</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.1.6">segemehl</requirement> 4 <requirement type="package" version="0.2.0">segemehl</requirement>
5 </requirements> 5 </requirements>
6 <stdio>
7 <regex match="Exit forced"
8 source="both"
9 level="fatal"
10 description="Execution halted." />
11 </stdio>
6 <command> 12 <command>
7 <![CDATA[ 13 <![CDATA[
8 ## prepare segemehl index if no reference genome is supplied 14 ## prepare segemehl index if no reference genome is supplied
9 temp_index = `mktemp`;
10 #if $refGenomeSource.genomeSource == "history": 15 #if $refGenomeSource.genomeSource == "history":
11 segemehl.x -x $temp_index -d $refGenomeSource.own_reference_genome; 16 mkdir ./temp_index/ &&
17 #set $temp_index = './temp_index/temp.idx'
18 segemehl.x -x $temp_index -d $refGenomeSource.own_reference_genome &&
12 #else: 19 #else:
13 #set $temp_index = $refGenomeSource.index.fields.index_path 20 #set $temp_index = $refGenomeSource.index.fields.index_path
14 #end if 21 #end if
15 22
16 23
18 segemehl.x 25 segemehl.x
19 26
20 ## number of threads 27 ## number of threads
21 -t "\${GALAXY_SLOTS:-12}" 28 -t "\${GALAXY_SLOTS:-12}"
22 29
23 ## db file path 30 #if $refGenomeSource.genomeSource == "history":
24 -d ${refGenomeSource.index.fields.db_path} 31 -d $refGenomeSource.own_reference_genome
32 #else:
33 -d ${refGenomeSource.index.fields.db_path}
34 #end if
25 35
26 -i $temp_index 36 -i $temp_index
27 37
28 ## check for single/pair-end 38 ## check for single/pair-end
29 #if str( $library.type ) == "single": 39 #if str( $library.type ) == "single":
30 #set $query_list = list() 40 #set $query_list = list()
31 ## prepare inputs 41 ## prepare inputs
32 #for $fastq in $library.reads: 42 #for $fastq in $library.input_query:
33 $query_list.append('%s' %($fastq.input_query)) 43 $query_list.append('%s' % $fastq )
34 #end for 44 #end for
35 -q "#echo ' '.join( $query_list )#" 45 -q "#echo ' '.join( $query_list )#"
36 #else 46 #else
37 ## prepare inputs 47 ## prepare inputs
38 48
59 #end if 69 #end if
60 $polyA 70 $polyA
61 $autoclip 71 $autoclip
62 $hardclip 72 $hardclip
63 $order 73 $order
74 $splits
75 #if $maxout:
76 --maxout $maxout
77 #end if
64 -s 78 -s
65 -o $segemehl_out 79
80 --minsplicecover $minsplicecover
81 --minfragscore $minfragscore
82 --minfraglen $minfraglen
83 --splicescorescale $splicescorescale
84
85 -o '$segemehl_out'
66 ]]> 86 ]]>
67 </command> 87 </command>
68 <stdio>
69 <regex match="Exit forced"
70 source="both"
71 level="fatal"
72 description="Execution halted." />
73 </stdio>
74 <inputs> 88 <inputs>
75
76 <conditional name="refGenomeSource"> 89 <conditional name="refGenomeSource">
77 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> 90 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
78 <option value="indexed">Use a built-in index</option> 91 <option value="indexed">Use a built-in index</option>
79 <option value="history">Use one from the history</option> 92 <option value="history">Use one from the history</option>
80 </param> 93 </param>
90 <validator type="no_options" message="No indexes are available for the selected input dataset"/> 103 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
91 </options> 104 </options>
92 </param> 105 </param>
93 </when> <!-- build-in --> 106 </when> <!-- build-in -->
94 <when value="history"> 107 <when value="history">
95 <param name="own_reference_genome" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" /> 108 <param name="own_reference_genome" type="data" format="fasta" label="Select the reference genome" />
96 </when> <!-- history --> 109 </when> <!-- history -->
97 </conditional> <!-- refGenomeSource --> 110 </conditional> <!-- refGenomeSource -->
98
99 111
100 <conditional name="library"> 112 <conditional name="library">
101 <param name="type" type="select" label="Is this library paired-end?"> 113 <param name="type" type="select" label="Is this library paired-end?">
102 <option value="single">Single-end</option> 114 <option value="single">Single-end</option>
103 <option value="paired">Paired-end</option> 115 <option value="paired">Paired-end</option>
104 </param> 116 </param>
105 <when value="single"> 117 <when value="single">
106 <repeat name="reads" title="FASTQ/FASTA files"> 118 <param name="input_query" type="data" multiple="True" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads in FASTQ/FASTA files" />
107 <param name="input_query" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads fasta/fastq file" />
108 </repeat>
109 </when> 119 </when>
110 <when value="paired"> 120 <when value="paired">
121 <!-- ToDo paired coolections -->
111 <repeat name="mate_list" title="Paired End Pairs" min="1"> 122 <repeat name="mate_list" title="Paired End Pairs" min="1">
112 <param name="first_strand_query" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads from first strand" /> 123 <param name="first_strand_query" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads from first strand" />
113 <param name="second_strand_query" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads from second strand" /> 124 <param name="second_strand_query" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads from second strand" />
114 </repeat> 125 </repeat>
115 <param name="maxinsertsize" type="integer" value="5000" label="Maximum size of the inserts (paired end)" help="default: 5000 (-I)" /> 126 <param name="maxinsertsize" type="integer" value="5000" label="Maximum size of the inserts (paired end)" help="default: 5000 (-I)" />
116 </when> 127 </when>
117 </conditional> 128 </conditional>
118 129
130 <param name="minsplicecover" type="integer" value="80" label="Min coverage for spliced transcripts" help="(--minsplicecover)" />
131 <param name="minfragscore" type="integer" value="18" label="Min coverage for spliced transcripts" help="(--minfragscore)" />
132 <param name="minfraglen" type="integer" value="20" label="Min length of a spliced fragment" help="(--minfraglen)" />
133 <param name="splicescorescale" type="float" value="1.0" label="Report spliced alignment with score greater than this scale times the score"
134 help="Report only if this value x score is larger than next best spliced alignment (--splicescorescale)" />
119 135
120 <param name="minsize" type="integer" value="12" size="5" label="Minimum size of queries" help="default: 12 (-m)"> 136 <param name="minsize" type="integer" value="12" min="1" label="Minimum size of queries" help="(-m)" />
121 <validator type="in_range" min="1"/> 137
122 </param> 138 <param name="maxout" type="integer" min="0" value="0" optional="True"
123 <param name="accuracy" type="integer" value="85" size="5" label="Min percentage of matches per read in semi-global alignment" help="default: 85 (-A)" > 139 label="Maximum number of alignments that will be reported" help="(--maxout)" />
124 <validator type="in_range" min="1" max="100"/> 140 <param name="accuracy" type="integer" value="85" min="1" max="100" label="Min percentage of matches per read in semi-global alignment" help="(-A)" />
125 </param> 141
126 <param name="hitstrategy" type="select" label="Hits to report?" help="(-H)"> 142 <param name="hitstrategy" type="select" label="Hits to report?" help="(-H)">
127 <option value="1">report only best scoring hits</option> 143 <option value="1">report only best scoring hits</option>
128 <option value="0">report all scoring hits</option> 144 <option value="0">report all scoring hits</option>
129 </param> 145 </param>
130 <param name="prime5" type="text" size="80" label="add 5' adapter" help="default: none (-Q)" /> 146 <param name="prime5" type="text" label="add 5' adapter" help="default: none (-Q)" />
131 <param name="prime3" type="text" size="80" label="add 3' adapter" help="default: none (-P)"/> 147 <param name="prime3" type="text" label="add 3' adapter" help="default: none (-P)"/>
132 <param name="polyA" type="boolean" truevalue="--polyA" falsevalue="" checked="false" label="Clip polyA tail" help="(-T)"/> 148 <param name="polyA" type="boolean" truevalue="--polyA" falsevalue="" checked="false" label="Clip polyA tail" help="(-T)"/>
133 <param name="autoclip" type="boolean" truevalue="--autoclip" falsevalue="" checked="false" label="Autoclip unknown 3prime adapter" help="(-Y)"/> 149 <param name="autoclip" type="boolean" truevalue="--autoclip" falsevalue="" checked="false" label="Autoclip unknown 3prime adapter" help="(-Y)"/>
134 <param name="hardclip" type="boolean" truevalue="--hardclip" falsevalue="" checked="false" label="Enable hard clipping" help="-C"/> 150 <param name="hardclip" type="boolean" truevalue="--hardclip" falsevalue="" checked="false" label="Enable hard clipping" help="(-C)"/>
135 <param name="order" type="boolean" truevalue="--order" falsevalue="" checked="false" label="Sorts the output by chromsome and position" help="(-O)"/> 151 <param name="order" type="boolean" truevalue="--order" falsevalue="" checked="false" label="Sorts the output by chromsome and position" help="(-O)"/>
152 <param name="splits" type="boolean" truevalue="--splits" falsevalue="" checked="false" label="Detect split/spliced reads" help="(--splits)"/>
136 </inputs> 153 </inputs>
137
138 <outputs> 154 <outputs>
139 <data format="sam" name="segemehl_out" label="Read alignments on ${on_string}"/> 155 <data format="sam" name="segemehl_out" label="Read alignments on ${on_string}"/>
140 </outputs> 156 </outputs>
157 <tests>
158 <test>
159 <param name="genomeSource" value="history" />
160 <param name="own_reference_genome" value="chr1.fa" />
161 <param name="library" value="single" />
162 <param name="input_query" value="test.fastq" />
163 <param name="splits" value="true" />
164 <output name="segemehl_out" file="testmap.sam" lines_diff="2" />
165 </test>
166 </tests>
141 <help> 167 <help>
142 <![CDATA[ 168 <![CDATA[
143 169
144 .. class:: infomark 170 .. class:: infomark
145 171