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comparison macros.xml @ 8:65c38d020fea draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
author rnateam
date Sun, 24 Sep 2017 14:28:47 -0400
parents cd8c76234b0c
children
comparison
equal deleted inserted replaced
7:1eafcc450052 8:65c38d020fea
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <macros> 2 <macros>
3 <token name="@VERSION@">2.1b</token> 3 <token name="@VERSION@">2.1b</token>
4 <xml name="db_prep">
5 <param name="seed_length" type="integer" min="0" max="100" value="18" label="Seed length for database indexing" help="(-L)"/>
6 <param name="max_pos" type="integer" min="0" max="100000" value="10000" label="Maximum number of positions to store for each k-mer for database indexing" help="With 0, all positions are stored (--max_pos)"/>
7 </xml>
8 <xml name="output_alignments">
9 <param name="print_all_reads" type="boolean" checked="false" truevalue="--print_all_reads" falsevalue="" label="Output null alignment strings for non-aligned reads"/>
10 <conditional name="blast">
11 <param name="blast_output" type="select" label="Output BLAST report?">
12 <option value="True">Yes</option>
13 <option value="False" selected="True">No</option>
14 </param>
15 <when value="True">
16 <param name="blast_format" type="select" label="BLAST-like format?">
17 <option value="0">pairwise (--blast '0')</option>
18 <option value="1">tabular BLAST -m 8 format (--blast '1')</option>
19 <option value="1 cigar">tabular + column for CIGAR (--blast '1 cigar')</option>
20 <option value="1 cigar qcov">tabular + columns for CIGAR and query coverage (--blast '1 cigar qcov')</option>
21 <option value="1 cigar qcov qstrand">tabular + columns for CIGAR, query coverage and strand (--blast '1 cigar qcov qstrand')</option>
22 </param>
23 </when>
24 <when value="False"/>
25 </conditional>
26 </xml>
27 <token name="@ALIGNMENTS@">
28 $report.print_all_reads
29 --sam
30 --SQ
31 #if $report.blast.blast_output == 'True'
32 --blast '$report.blast.blast_format'
33 #end if
34 </token>
4 </macros> 35 </macros>