Mercurial > repos > jjohnson > defuse

comparison defuse.xml @ 46:e500b50b72fd draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author jjohnson
date Thu, 19 Oct 2017 10:05:54 -0400
parents aedaa66483f1
children
comparison
equal deleted inserted replaced
45:aedaa66483f1 46:e500b50b72fd
7 <expand macro="defuse_requirement" /> 7 <expand macro="defuse_requirement" />
8 </requirements> 8 </requirements>
9 <command><![CDATA[ 9 <command><![CDATA[
10 #if $defuse_out.__str__ != 'None': 10 #if $defuse_out.__str__ != 'None':
11 ## ln to output_dir in from_work_dir 11 ## ln to output_dir in from_work_dir
12 mkdir -p $defuse_out.dataset.extra_files_path && 12 mkdir -p $defuse_out.files_path &&
13 ln -s $defuse_out.dataset.extra_files_path output_dir && 13 ln -s $defuse_out.files_path output_dir &&
14 #else 14 #else
15 mkdir -p output_dir && 15 mkdir -p output_dir &&
16 #end if 16 #end if
17 ## Put executable paths in config file 17 ## Put executable paths in config file
18 $__tool_directory__/config_sub.sh $defuse_config output_dir/defuse.cfg && 18 $__tool_directory__/config_sub.sh $defuse_config output_dir/defuse.cfg &&
19 ## copy config to output 19 ## copy config to output
20 cp defuse.cfg $config_txt && 20 cp output_dir/defuse.cfg $config_txt &&
21 ## make a data_dir and ln -s the input fastq 21 ## make a data_dir and ln -s the input fastq
22 mkdir -p data_dir && 22 mkdir -p data_dir &&
23 ln -s "$left_pairendreads" data_dir/reads_1.fastq && 23 ln -s "$left_pairendreads" data_dir/reads_1.fastq &&
24 ln -s "$right_pairendreads" data_dir/reads_2.fastq && 24 ln -s "$right_pairendreads" data_dir/reads_2.fastq &&
25 ## run 25 ## run
26 perl defuse_run.pl --name "$library_name" --config defuse.cfg -1 data_dir/reads_1.fastq -2 data_dir/reads_2.fastq -o output_dir -p \$GALAXY_SLOTS && 26 DATASET_DIRECTORY=`grep '^dataset_directory' output_dir/defuse.cfg | awk '{print \$NF}'` &&
27 defuse_run.pl --name "$library_name" --config output_dir/defuse.cfg --dataset \$DATASET_DIRECTORY -1 data_dir/reads_1.fastq -2 data_dir/reads_2.fastq -o output_dir -p \$GALAXY_SLOTS &&
27 grep -v cluster_id output_dir/results.filtered.tsv | awk '{print $1}' > cluster_id_list && 28 grep -v cluster_id output_dir/results.filtered.tsv | awk '{print $1}' > cluster_id_list &&
28 get_fusion_fastq.pl --list cluster_id_list --output output_dir --fastq1 results.fusions_1.fq --fastq2 results.fusions_2.fq && 29 get_fusion_fastq.pl --list cluster_id_list --output output_dir --fastq1 results.fusions_1.fq --fastq2 results.fusions_2.fq &&
29 cp output_dir/results.* . && 30 cp output_dir/results.* . &&
30 cp `find output_dir -name defuse.log` $defuse_log 31 cp `find -L output_dir -name defuse.log` $defuse_log
31 #if $defuse_out.__str__ != 'None': 32 #if $defuse_out.__str__ != 'None':
32 && $__tool_directory__/make_html.sh $defuse_out $defuse_out.dataset.extra_files_path 33 && $__tool_directory__/make_html.sh $defuse_out $defuse_out.files_path
33 #end if 34 #end if
34 ]]></command> 35 ]]></command>
35 <inputs> 36 <inputs>
36 <param name="left_pairendreads" type="data" format="fastq" label="left part of read pairs" help="The left and right reads pairs must be in the same order, and not have any unpaired reads. (FASTQ interlacer will pair reads and remove the unpaired. FASTQ de-interlacer will separate the result into left and right reads.)"/> 37 <param name="left_pairendreads" type="data" format="fastq" label="left part of read pairs" help="The left and right reads pairs must be in the same order, and not have any unpaired reads. (FASTQ interlacer will pair reads and remove the unpaired. FASTQ de-interlacer will separate the result into left and right reads.)"/>
37 <param name="right_pairendreads" type="data" format="fastq" label="right part of read pairs" help="In the same order as the left reads"/> 38 <param name="right_pairendreads" type="data" format="fastq" label="right part of read pairs" help="In the same order as the left reads"/>
108 </when> <!-- full --> 109 </when> <!-- full -->
109 </conditional> <!-- defuse_param --> 110 </conditional> <!-- defuse_param -->
110 <param name="keep_output" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Save DeFuse working directory files" 111 <param name="keep_output" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Save DeFuse working directory files"
111 help="The defuse output working directory can be helpful for determining errors that may have occurred during the run, 112 help="The defuse output working directory can be helpful for determining errors that may have occurred during the run,
112 but they require considerable diskspace, and should be deleted and purged when no longer needed."/> 113 but they require considerable diskspace, and should be deleted and purged when no longer needed."/>
113 <param name="breakpoints_bam" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Generate a Bam file for the fusions"/>
114 <param name="do_get_reads" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Run get_reads on each cluster"/>
115 </inputs> 114 </inputs>
116 <outputs> 115 <outputs>
117 <data format="txt" name="config_txt" label="${tool.name} on ${on_string}: config.txt"/> 116 <data format="txt" name="config_txt" label="${tool.name} on ${on_string}: config.txt"/>
118 <data format="txt" name="defuse_log" label="${tool.name} on ${on_string}: defuse.log" /> 117 <data format="txt" name="defuse_log" label="${tool.name} on ${on_string}: defuse.log" />
119 <data format="html" name="defuse_out" label="${tool.name} on ${on_string}: defuse_output (purge when no longer needed)"> 118 <data format="html" name="defuse_out" label="${tool.name} on ${on_string}: defuse_output (purge when no longer needed)">