Mercurial > repos > iuc > colibread_kissplice
comparison macros.xml @ 0:4acdd256cc12 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
author | iuc |
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date | Fri, 20 Oct 2017 03:14:17 -0400 |
parents | |
children | d5b4404c4788 |
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-1:000000000000 | 0:4acdd256cc12 |
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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> |