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annotate 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
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cd8c76234b0c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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1 <?xml version="1.0" ?>
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2 <macros>
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3 <token name="@VERSION@">2.1b</token>
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4 <xml name="db_prep">
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5 <param name="seed_length" type="integer" min="0" max="100" value="18" label="Seed length for database indexing" help="(-L)"/>
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
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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)"/>
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
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7 </xml>
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8 <xml name="output_alignments">
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9 <param name="print_all_reads" type="boolean" checked="false" truevalue="--print_all_reads" falsevalue="" label="Output null alignment strings for non-aligned reads"/>
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10 <conditional name="blast">
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11 <param name="blast_output" type="select" label="Output BLAST report?">
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
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12 <option value="True">Yes</option>
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13 <option value="False" selected="True">No</option>
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14 </param>
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15 <when value="True">
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16 <param name="blast_format" type="select" label="BLAST-like format?">
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17 <option value="0">pairwise (--blast '0')</option>
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18 <option value="1">tabular BLAST -m 8 format (--blast '1')</option>
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19 <option value="1 cigar">tabular + column for CIGAR (--blast '1 cigar')</option>
65c38d020fea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 1739cab238d13107d96acd9f87700869fa9d3193-dirty
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20 <option value="1 cigar qcov">tabular + columns for CIGAR and query coverage (--blast '1 cigar qcov')</option>
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21 <option value="1 cigar qcov qstrand">tabular + columns for CIGAR, query coverage and strand (--blast '1 cigar qcov qstrand')</option>
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22 </param>
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23 </when>
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24 <when value="False"/>
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25 </conditional>
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26 </xml>
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27 <token name="@ALIGNMENTS@">
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28 $report.print_all_reads
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29 --sam
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30 --SQ
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31 #if $report.blast.blast_output == 'True'
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32 --blast '$report.blast.blast_format'
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33 #end if
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34 </token>
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35 </macros>