Mercurial > repos > thanhlv > bin3c

comparison mkmap.xml @ 14:8d920f67589d draft

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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit fd6117dcead9ad542ed6afd526adab8d1200fbcf-dirty
author thanhlv
date Mon, 14 Oct 2019 08:49:53 -0400
parents f3135aeac82c
children cdfc397e7b0f
comparison
equal deleted inserted replaced
13:f3135aeac82c 14:8d920f67589d
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="version_command" /> 7 <expand macro="version_command" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 bin3C mkmap 9 bin3C mkmap
10 $clobber
11 --max-image $max_image 10 --max-image $max_image
12 --min-extent $min_extent 11 --min-extent $min_extent
13 --min-reflen $min_reflen 12 --min-reflen $min_reflen
14 --min-signal $min_signal 13 --min-signal $min_signal
15 $eta 14 #if str($bin_size) != "0":
16 --bin-size $bin_size 15 --bin-size $bin_size
16 #end if
17 --min-insert $min_insert 17 --min-insert $min_insert
18 --min-mapq $min_mapq 18 --min-mapq $min_mapq
19 $eta
19 --strong $strong 20 --strong $strong
20 #if str($neb_name) != "": 21 #if str($neb_name) != "":
21 #for $enzyme in str($neb_name).split(',') 22 #for $enzyme in str($neb_name).split(',')
22 -e $enzyme 23 -e $enzyme
23 #end for 24 #end for
26 ]]></command> 27 ]]></command>
27 28
28 <inputs> 29 <inputs>
29 <param name="ref" type="data" format="fasta,fastaq.gz" label="Reference fasta sequence" /> 30 <param name="ref" type="data" format="fasta,fastaq.gz" label="Reference fasta sequence" />
30 <param name="bam" type="data" format="bam" label="Input bam file in query order" /> 31 <param name="bam" type="data" format="bam" label="Input bam file in query order" />
31 <param name="clobber" type="boolean" truevalue="--clobber" falsevalue="" checked="false" label="Clobber existing files" />
32 <param name="max_image" type="integer" min="1" value="4000" label="Maximum image size for plots"/> 32 <param name="max_image" type="integer" min="1" value="4000" label="Maximum image size for plots"/>
33 <param name="min_extent" type="integer" min="1" value="50000" label="Minimum cluster extent used in output"/> 33 <param name="min_extent" type="integer" min="1" value="50000" label="Minimum cluster extent used in output"/>
34 <param name="min_reflen" type="integer" min="1" value="1000" label="Minimum acceptable reference length"/> 34 <param name="min_reflen" type="integer" min="1" value="1000" label="Minimum acceptable reference length"/>
35 <param name="min_signal" type="integer" min="1" value="5" label="Minimum acceptable signal"/> 35 <param name="min_signal" type="integer" min="1" value="5" label="Minimum acceptable signal"/>
36 <param name="eta" type="boolean" truevalue="--eta" falsevalue="" checked="false" label="Re-count bam alignments to provide an ETA" /> 36 <param name="eta" type="boolean" truevalue="--eta" falsevalue="" checked="false" label="Re-count bam alignments to provide an ETA" />