Mercurial > repos > pjbriggs > pal_finder

comparison pal_finder_wrapper.xml @ 1:771ebe02636f draft

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Uploaded version 0.02.04.2: fix bug that causes tool to fail when prefix includes spaces; add explicit dependency on Perl 5.16.3.
author pjbriggs
date Mon, 23 Mar 2015 07:01:37 -0400
parents 3f908e7fff4f
children b6ccc7dd7b02
comparison
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0:3f908e7fff4f 1:771ebe02636f
1 <tool id="microsat_pal_finder" name="pal_finder" version="0.02.04.1"> 1 <tool id="microsat_pal_finder" name="pal_finder" version="0.02.04.2">
2 <description>Find microsatellite repeat elements sequencing reads and design PCR primers to amplify them</description> 2 <description>Find microsatellite repeat elements sequencing reads and design PCR primers to amplify them</description>
3 <command interpreter="bash">pal_finder_wrapper.sh 3 <command interpreter="bash">pal_finder_wrapper.sh
4 #if str( $platform.platform_type ) == "illumina" 4 #if str( $platform.platform_type ) == "illumina"
5 $platform.input_fastq_r1 $platform.input_fastq_r2 5 $platform.input_fastq_r1 $platform.input_fastq_r2
6 #else 6 #else
11 --filter_microsats $output_filtered_microsats 11 --filter_microsats $output_filtered_microsats
12 #end if 12 #end if
13 #if $keep_config_file 13 #if $keep_config_file
14 --output_config_file $output_config_file 14 --output_config_file $output_config_file
15 #end if 15 #end if
16 --primer-prefix $primer_prefix 16 --primer-prefix "$primer_prefix"
17 --2merMinReps $min_2mer_repeats 17 --2merMinReps $min_2mer_repeats
18 --3merMinReps $min_3mer_repeats 18 --3merMinReps $min_3mer_repeats
19 --4merMinReps $min_4mer_repeats 19 --4merMinReps $min_4mer_repeats
20 --5merMinReps $min_5mer_repeats 20 --5merMinReps $min_5mer_repeats
21 --6merMinReps $min_6mer_repeats 21 --6merMinReps $min_6mer_repeats
35 #if str( $mispriming.mispriming_options ) == "custom" 35 #if str( $mispriming.mispriming_options ) == "custom"
36 --primer-mispriming-library $mispriming.mispriming_library 36 --primer-mispriming-library $mispriming.mispriming_library
37 #end if 37 #end if
38 </command> 38 </command>
39 <requirements> 39 <requirements>
40 <requirement type="package" version="5.16.3">perl</requirement>
40 <requirement type="package" version="0.02.04">pal_finder</requirement> 41 <requirement type="package" version="0.02.04">pal_finder</requirement>
41 <requirement type="package" version="2.0.0">primer3_core</requirement> 42 <requirement type="package" version="2.0.0">primer3_core</requirement>
42 </requirements> 43 </requirements>
43 <inputs> 44 <inputs>
44 <param name="primer_prefix" type="text" value="test" size="25" label="Primer prefix" help="This prefix will be added to the beginning of all primer names" /> 45 <param name="primer_prefix" type="text" value="test" size="25" label="Primer prefix" help="This prefix will be added to the beginning of all primer names" />