Mercurial > repos > big-tiandm > mirplant2
comparison preProcess.xml @ 50:7b5a48b972e9 draft
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author | big-tiandm |
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date | Fri, 05 Dec 2014 00:11:02 -0500 |
parents | c75593f79aa9 |
children | 8b8c356e6db5 |
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49:f008ab2cadc6 | 50:7b5a48b972e9 |
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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> |