Mercurial > repos > iuc > colibread_mapsembler2

comparison macros.xml @ 0:265fa5effd4d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
author iuc
date Fri, 20 Oct 2017 03:15:10 -0400
parents
children 00fd0b4274fd
comparison
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-1:000000000000 0:265fa5effd4d
1 <macros>
2 <token name="@discosnp_single_reads@"><![CDATA[
3 #for $input in $input_type_options.list_reads
4 #set $filename = str($input) + "." + $input.ext
5 ln -sf '${input}' '${filename}' &&
6 echo '${filename}' >> input.lst &&
7 #end for
8 ]]></token>
9 <token name="@discosnp_paired_reads@"><![CDATA[
10 #for $i, $paired in enumerate( $input_type_options.list_paired_reads )
11
12 #set $filenameFWD = str($paired.forward) + "." + $paired.forward.ext
13 ln -sf '${paired.forward}' '${filenameFWD}' &&
14
15 #set $filenameREV = str($paired.reverse) + "." + $paired.reverse.ext
16 ln -sf '${paired.reverse}' '${filenameREV}' &&
17
18 echo '${filenameFWD}' > "paired_${i}.lst" &&
19 echo '${filenameREV}' >> "paired_${i}.lst" &&
20 echo "paired_${i}.lst" >> input.lst &&
21
22 #end for
23 ]]></token>
24 <token name="@lordec_inputs@"><![CDATA[
25 -2 "${ ",".join(['%s' % file for file in $program_type_choice.inputs]) }"
26 -i '${program_type_choice.i}'
27 -k ${program_type_choice.k}
28 -s ${program_type_choice.s}
29 ]]></token>
30 <xml name="lordec_inputs">
31 <param name="inputs" argument="-2" type="data" format="fasta,fastq.gz,fastq" multiple="true" label="Short read FASTA/Q files" />
32 <param argument="-i" type="data" format="fasta,fastq.gz,fastq" label="Long read FASTA/Q file" help="PacBio reads files" />
33 <param argument="-k" type="integer" label="Size of kmers" value="31" help="Only uneven number"/>
34 <param argument="-s" type="integer" label="Solidity abundance threshold for k-mers" value="4" />
35 </xml>
36 <xml name="citations">
37 <citations>
38 <yield/>
39 <citation type="doi">10.1186/s13742-015-0105-2</citation>
40 </citations>
41 </xml>
42 </macros>