Mercurial > repos > thanhlv > bin3c

comparison mkmap.xml @ 4:a8ebe008f31a draft

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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 70fbc98b2ff2be134400e4dc0df1ed60458d0604
author thanhlv
date Thu, 03 Oct 2019 06:33:55 -0400
parents a8600e2b39b2
children 0c844be874b5
comparison
equal deleted inserted replaced
3:a8600e2b39b2 4:a8ebe008f31a
15 $eta 15 $eta
16 --bin-size $bin_size 16 --bin-size $bin_size
17 --min-insert $min_insert 17 --min-insert $min_insert
18 --min-mapq $min_mapq 18 --min-mapq $min_mapq
19 --strong $strong 19 --strong $strong
20 #if neb_name != "" 20 #if $neb_name != ""
21 --enzyme $neb_name 21 #set $_neb_name = ' -e '.join( str( $neb_name ).split( ';' ) )
22 -e ${_neb_name}
22 #end if 23 #end if
23 $ref $bam out 24 $ref $bam out
24 ]]></command> 25 ]]></command>
25 26
26 <inputs> 27 <inputs>
35 <param name="bin_size" type="integer" min="0" value="0" label="Size of bins for windows extent maps" /> 36 <param name="bin_size" type="integer" min="0" value="0" label="Size of bins for windows extent maps" />
36 <param name="min_insert" type="integer" min="0" value="0" label="Minimum pair separation" /> 37 <param name="min_insert" type="integer" min="0" value="0" label="Minimum pair separation" />
37 <param name="min_mapq" type="integer" min="0" value="60" label="Minimum acceptable mapping quality" /> 38 <param name="min_mapq" type="integer" min="0" value="60" label="Minimum acceptable mapping quality" />
38 <param name="strong" type="integer" min="1" value="10" label="Accepted alignments must being N matches" /> 39 <param name="strong" type="integer" min="1" value="10" label="Accepted alignments must being N matches" />
39 <param name="neb_name" type="text" value="" label="Case-sensitive NEB enzyme name. Use multiple times for 40 <param name="neb_name" type="text" value="" label="Case-sensitive NEB enzyme name. Use multiple times for
40 multiple enzymes" /> 41 multiple enzymes", help="Use ; to separate multiple enzymes, e.g enzyme1;enzyme2" />
41 </inputs> 42 </inputs>
42 43
43 <outputs> 44 <outputs>
44 <data name="contact_map" format="tar.gz" label="{tool.name} on ${on_string} Contact map" from_work_dir="out/contact_map.p.gz"/> 45 <data name="contact_map" format="tar.gz" label="{tool.name} on ${on_string} Contact map" from_work_dir="out/contact_map.p.gz"/>
45 <data name="log" format="text" label="{tool.name} on ${on_string} Log" from_work_dir="out/bin3C.log"/> 46 <data name="log" format="text" label="{tool.name} on ${on_string} Log" from_work_dir="out/bin3C.log"/>