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comparison preProcess.xml @ 50:7b5a48b972e9 draft

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author big-tiandm
date Fri, 05 Dec 2014 00:11:02 -0500
parents c75593f79aa9
children 8b8c356e6db5
comparison
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49:f008ab2cadc6 50:7b5a48b972e9
10 <requirement type="package" version="2.1.8">ViennaRNA</requirement> 10 <requirement type="package" version="2.1.8">ViennaRNA</requirement>
11 </requirements> 11 </requirements>
12 12
13 <!--command interpreter="perl">miPlant.pl -i $input -format $format -gfa $gfa -idx $index -pre $pre -mat $mat -rfam $rfam -idx2 $idx2 -D $D -a $a -M $M -min $min -max $max -mis $mis -e $e -f $f -v $v -r $r -dis $dis -flank $flank -mfe $mfe -t $t -o $output</command--> 13 <!--command interpreter="perl">miPlant.pl -i $input -format $format -gfa $gfa -idx $index -pre $pre -mat $mat -rfam $rfam -idx2 $idx2 -D $D -a $a -M $M -min $min -max $max -mis $mis -e $e -f $f -v $v -r $r -dis $dis -flank $flank -mfe $mfe -t $t -o $output</command-->
14 14
15 <command interpreter="perl">miRPlant.pl 15 <command interpreter="perl">preProcess.pl
16 ## Change this to accommodate the number of threads you have available. 16 ## Change this to accommodate the number of threads you have available.
17 -t \${GALAXY_SLOTS:-4} 17 -t \${GALAXY_SLOTS:-4}
18 -path \$SCRIPT_PATH 18 -path \$SCRIPT_PATH
19 19
20 #for $j, $s in enumerate( $series ) 20 #for $j, $s in enumerate( $series )
23 -tag ${s.tag} 23 -tag ${s.tag}
24 #end for 24 #end for
25 25
26 ## Do or not annotate rfam non-miRNA RNAs 26 ## Do or not annotate rfam non-miRNA RNAs
27 #if $params.annotate_rfam == "yes": 27 #if $params.annotate_rfam == "yes":
28 -rfam $rfam 28 ## prepare Rfam bowtie index
29 #set rfam_index_path = ''
30 #if str($params.annotate_rfam.reference_rfam.source) == "history":
31 bowtie-build "$params.annotate_rfam.reference_rfam.own_file" rfam; ln -s "$params.annotate_rfam.reference_rfam.own_file" rfam.fa;
32 #set rfam_index_path = 'rfam'
33 #else:
34 #set rfam_index_path = $params.annotate_rfam.reference_rfam.index.fields.path
35 #end if
36
37 -rfam ${rfam_index_path}.fa -idx2 $rfam_index_path -v $v
29 #end if 38 #end if
30 39
31 ## prepare bowtie index 40 ## prepare bowtie index
32 #set index_path = '' 41 #set index_path = ''
33 #if str($reference_genome.source) == "history": 42 #if str($reference_genome.source) == "history":
35 #set index_path = 'genome' 44 #set index_path = 'genome'
36 #else: 45 #else:
37 #set index_path = $reference_genome.index.fields.path 46 #set index_path = $reference_genome.index.fields.path
38 #end if 47 #end if
39 48
40 -format $format -gfa ${index_path}.fa -idx $index_path -a $a -M $mapnt -min $min -max $max -mis $mismatch -v $v > run.log 49 -format $format -gfa ${index_path}.fa -idx $index_path -phred $phred -a $a -M $mapnt -min $min -max $max -mis $mismatch > run.log
41 </command> 50 </command>
42 51
43 <inputs> 52 <inputs>
44 53
45 <repeat name="series" title="Series"> 54 <repeat name="series" title="Series">
73 </when> 82 </when>
74 </conditional> 83 </conditional>
75 84
76 <!--param name="gfa" type="data" label="genome sequence fasta file"/--> 85 <!--param name="gfa" type="data" label="genome sequence fasta file"/-->
77 <!--param type="data" name="index" label="genome sequence bowtie index"/--> 86 <!--param type="data" name="index" label="genome sequence bowtie index"/-->
87 <param name="phred" type="select" lable="input quals are Phred+64 or Phred+33" multiple="false">
88 <option value="64">Phred+64</option>
89 <option value="33" selected="true">Phred+33</option>
90 </param>
78 <param name="a" type="text" value="ATCTCGTATG" label="3' adapter sequence" /> 91 <param name="a" type="text" value="ATCTCGTATG" label="3' adapter sequence" />
79 <param name="mapnt" type="integer" value="8" label="minimum adapter map nts" /> 92 <param name="mapnt" type="integer" value="8" label="minimum adapter map nts" />
80 <param name="min" type="integer" value="19" label="minimum microRNA length" /> 93 <param name="min" type="integer" value="19" label="minimum microRNA length" />
81 <param name="max" type="integer" value="28" label="maximum microRNA length" /> 94 <param name="max" type="integer" value="28" label="maximum microRNA length" />
82 <param name="mismatch" type="integer" value="0" label="number of allowed mismatches when mapping reads to genome" /> 95 <param name="mismatch" type="integer" value="0" label="number of allowed mismatches when mapping reads to genome" />
85 <param name="annotate_rfam" type="select" label="annotate rfam nocoding RNAs(excluding miRNA)"> 98 <param name="annotate_rfam" type="select" label="annotate rfam nocoding RNAs(excluding miRNA)">
86 <option value="yes" selected="true">yes</option> 99 <option value="yes" selected="true">yes</option>
87 <option value="no">no</option> 100 <option value="no">no</option>
88 </param> 101 </param>
89 <when value="yes"> 102 <when value="yes">
90 <param name="rfam" type="data" label="rfam sequence file" /> 103 <!--param name="rfam" type="data" label="rfam sequence file" /-->
91 <!--param type="data" name="idx2" label="rfam sequence bowtie index " --> 104 <when value="yes">
105 <!--param name="rfam" type="data" label="rfam sequence file" /-->
106 <conditional name="reference_rfam">
107 <param name="source" 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">
108 <option value="indexed">Use a built-in index</option>
109 <option value="history">Use one from the history</option>
110 </param>
111 <when value="indexed">
112 <param name="index" type="select" label="Select a reference" help="If your reference of interest is not listed, contact the Galaxy team">
113 <options from_data_table="rfam_bowtie_indexes">
114 <filter type="sort_by" column="2"/>
115 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
116 </options>
117 </param>
118 </when>
119 <when value="history">
120 <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select the reference" />
121 </when>
122 </conditional>
123
92 <param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches for rfam mapping"/> 124 <param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches for rfam mapping"/>
93 </when> 125 </when>
94 </conditional> <!-- params --> 126 </conditional> <!-- params -->
95 127
96 </inputs> 128 </inputs>
110 <filter>(params['annotate_rfam'] == 'Yes')</filter> 142 <filter>(params['annotate_rfam'] == 'Yes')</filter>
111 </data> 143 </data>
112 <data format="txt" name="Rfam not mapped FASTA file" from_work_dir="preProcess/rfam_match/rfam_not_mapped.fa" label="${tool.name} on ${on_string}: Rfam not mapped FASTA file"> 144 <data format="txt" name="Rfam not mapped FASTA file" from_work_dir="preProcess/rfam_match/rfam_not_mapped.fa" label="${tool.name} on ${on_string}: Rfam not mapped FASTA file">
113 <filter>(params['annotate_rfam'] == 'Yes')</filter> 145 <filter>(params['annotate_rfam'] == 'Yes')</filter>
114 </data> 146 </data>
147 <data format="html" name="input config" from_work_dir="preProcess/input_config" label="${tool.name} on ${on_string}: input config"/>
148
115 </outputs> 149 </outputs>
116 150
117 <help> 151 <help>
118 152
119 </help> 153 </help>