sortmerna: sortmerna.xml annotate

annotate sortmerna.xml @ 12:67a87a218aa4 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc

author	rnateam
date	Wed, 20 Mar 2019 03:00:33 -0400
parents	035f14f54ba7
children

rev	line source
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	1 <tool id="bg_sortmerna" name="Filter with SortMeRNA" version="@VERSION@.6">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	2 <description>of ribosomal RNAs in metatranscriptomic data</description>
9 fccaaa82d221 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 65d322f9ab2f24d65b307f3553589149a1d678d5 rnateam parents: 8 diff changeset	3 <macros>
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	4 <token name="@VERSION@">2.1b</token>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	5 <xml name="db_prep">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	6 <param name="seed_length" type="integer" min="0" max="100" value="18" label="Seed length for database indexing" help="(-L)"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	7 <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)"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	8 </xml>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	9 <xml name="output_alignments">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	10 <param name="print_all_reads" type="boolean" checked="false" truevalue="--print_all_reads" falsevalue="" label="Output null alignment strings for non-aligned reads"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	11 <conditional name="blast">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	12 <param name="blast_output" type="select" label="Output BLAST report?">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	13 <option value="True">Yes</option>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	14 <option value="False" selected="True">No</option>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	15 </param>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	16 <when value="True">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	17 <param name="blast_format" type="select" label="BLAST-like format?">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	18 <option value="0">pairwise (--blast '0')</option>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	19 <option value="1">tabular BLAST -m 8 format (--blast '1')</option>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	20 <option value="1 cigar">tabular + column for CIGAR (--blast '1 cigar')</option>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	21 <option value="1 cigar qcov">tabular + columns for CIGAR and query coverage (--blast '1 cigar qcov')</option>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	22 <option value="1 cigar qcov qstrand">tabular + columns for CIGAR, query coverage and strand (--blast '1 cigar qcov qstrand')</option>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	23 </param>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	24 </when>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	25 <when value="False"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	26 </conditional>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	27 </xml>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	28 <token name="@ALIGNMENTS@">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	29 $report.print_all_reads
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	30 --sam
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	31 --SQ
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	32 #if $report.blast.blast_output == 'True'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	33 --blast '$report.blast.blast_format'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	34 #end if
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	35 </token>
9 fccaaa82d221 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 65d322f9ab2f24d65b307f3553589149a1d678d5 rnateam parents: 8 diff changeset	36 </macros>
3 42509ccf8f59 Uploaded iuc parents: diff changeset	37 <requirements>
9 fccaaa82d221 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 65d322f9ab2f24d65b307f3553589149a1d678d5 rnateam parents: 8 diff changeset	38 <requirement type="package" version="@VERSION@">sortmerna</requirement>
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	39 <requirement type="package" version="1.5">samtools</requirement>
3 42509ccf8f59 Uploaded iuc parents: diff changeset	40 </requirements>
42509ccf8f59 Uploaded iuc parents: diff changeset	41 <stdio>
42509ccf8f59 Uploaded iuc parents: diff changeset	42 <regex match="This program builds a Burst trie on an input rRNA database"
42509ccf8f59 Uploaded iuc parents: diff changeset	43 source="both"
42509ccf8f59 Uploaded iuc parents: diff changeset	44 level="fatal"
42509ccf8f59 Uploaded iuc parents: diff changeset	45 description="Buildtrie program failed to execute." />
42509ccf8f59 Uploaded iuc parents: diff changeset	46 <regex match="The database name"
42509ccf8f59 Uploaded iuc parents: diff changeset	47 source="both"
42509ccf8f59 Uploaded iuc parents: diff changeset	48 level="fatal"
42509ccf8f59 Uploaded iuc parents: diff changeset	49 description="The database ${databases} has not been preprocessed using buildtrie before using SortMeRNA." />
6 97f73e0566c9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707 rnateam parents: 5 diff changeset	50 <regex match="ERROR"
97f73e0566c9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707 rnateam parents: 5 diff changeset	51 source="both"
97f73e0566c9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707 rnateam parents: 5 diff changeset	52 level="fatal"
97f73e0566c9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707 rnateam parents: 5 diff changeset	53 description="ERROR" />
3 42509ccf8f59 Uploaded iuc parents: diff changeset	54 </stdio>
42509ccf8f59 Uploaded iuc parents: diff changeset	55 <version_command>
42509ccf8f59 Uploaded iuc parents: diff changeset	56 <![CDATA[
42509ccf8f59 Uploaded iuc parents: diff changeset	57 sortmerna --version 2>&1\|grep 'SortMeRNA version'
42509ccf8f59 Uploaded iuc parents: diff changeset	58 ]]>
42509ccf8f59 Uploaded iuc parents: diff changeset	59 </version_command>
42509ccf8f59 Uploaded iuc parents: diff changeset	60 <command>
42509ccf8f59 Uploaded iuc parents: diff changeset	61 <![CDATA[
42509ccf8f59 Uploaded iuc parents: diff changeset	62 #set $ref = ''
42509ccf8f59 Uploaded iuc parents: diff changeset	63 #set $sep=''
5 233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	64 #if str( $databases_type.databases_selector ) == 'history'
3 42509ccf8f59 Uploaded iuc parents: diff changeset	65 #for $db in $databases_type.database_name
42509ccf8f59 Uploaded iuc parents: diff changeset	66 #set $ref += $sep + str($db) + ',' + $os.path.splitext($os.path.basename(str($db)))[0]
42509ccf8f59 Uploaded iuc parents: diff changeset	67 #set $sep = ':'
42509ccf8f59 Uploaded iuc parents: diff changeset	68 #end for
5 233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	69 #else if str( $databases_type.databases_selector ) == 'cached_to_index'
11 035f14f54ba7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4241c1d4b05a177bd2c74f5a139f51d4f65e0b55 rnateam parents: 10 diff changeset	70 #for $db in $databases_type.input_databases.fields.path.split(",")
035f14f54ba7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4241c1d4b05a177bd2c74f5a139f51d4f65e0b55 rnateam parents: 10 diff changeset	71 #set $ref += $sep + $db + ',' + $os.path.splitext($db)[0] + '-reindexed'
5 233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	72 #set $sep = ':'
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	73 #end for
11 035f14f54ba7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4241c1d4b05a177bd2c74f5a139f51d4f65e0b55 rnateam parents: 10 diff changeset	74 #else
035f14f54ba7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4241c1d4b05a177bd2c74f5a139f51d4f65e0b55 rnateam parents: 10 diff changeset	75 #for $db in $databases_type.input_databases.fields.path.split(",")
035f14f54ba7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4241c1d4b05a177bd2c74f5a139f51d4f65e0b55 rnateam parents: 10 diff changeset	76 #set $ref += $sep + $db + ',' + $os.path.splitext($db)[0]
3 42509ccf8f59 Uploaded iuc parents: diff changeset	77 #set $sep = ':'
42509ccf8f59 Uploaded iuc parents: diff changeset	78 #end for
42509ccf8f59 Uploaded iuc parents: diff changeset	79 #end if
5 233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	80
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	81 #if str( $databases_type.databases_selector ) != 'cached'
5 233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	82 indexdb_rna
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	83 --ref '$ref'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	84 -L '$databases_type.seed_length'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	85 --max_pos '$databases_type.max_pos'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	86 &&
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	87 #end if
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	88
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	89 #if str( $sequencing_type.sequencing_type_selector ) == 'paired'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	90 merge-paired-reads.sh
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	91 '$sequencing_type.forward_reads'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	92 '$sequencing_type.reverse_reads'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	93 merged-reads
5 233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	94 &&
3 42509ccf8f59 Uploaded iuc parents: diff changeset	95 #end if
5 233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	96
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	97 sortmerna
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	98 --ref '$ref'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	99 --aligned 'aligned'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	100 #if str( $sequencing_type.sequencing_type_selector ) == 'paired'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	101 --reads 'merged-reads'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	102 $sequencing_type.paired_type
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	103 #else
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	104 --reads '$sequencing_type.reads'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	105 #end if
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	106 $strand_search
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	107 $log
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	108 $aligned_fastx.aligned_fastx_selector
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	109 #if $aligned_fastx.aligned_fastx_selector == '--fastx'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	110 #if $aligned_fastx.other
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	111 --other 'unaligned'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	112 #end if
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	113 #end if
5 233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	114 #if $report.report_type == 'best'
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	115 @ALIGNMENTS@
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	116 #if $report.otu.otu_map == 'True'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	117 --otu_map
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	118 --id '$report.otu.id'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	119 --coverage '$report.otu.coverage'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	120 $report.otu.de_novo_otu
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	121 #end if
6 97f73e0566c9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707 rnateam parents: 5 diff changeset	122 #if $report.report_best.report_best_type == '1'
5 233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	123 --best 1
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	124 --min_lis '$report.report_best.report_best_min_lis'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	125 #else
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	126 --best '$report.report_best.report_best_value'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	127 --min_lis '$report.report_best.report_best_min_lis'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	128 #end if
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	129 #elif $report.report_type == 'num_alignments'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	130 @ALIGNMENTS@
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	131 #if $report.report_num_alignments.report_num_alignments_type == 'other_value'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	132 --num_alignments '$report.report_num_alignments.report_num_alignments_value'
5 233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	133 #else
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	134 --num_alignments '$report.report_num_alignments.report_num_alignments_type'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	135 #end if
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	136 #end if
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	137 -e '$e_value'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	138 --match '$match'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	139 --mismatch '$mismatch'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	140 --gap_open '$gap_open'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	141 --gap_ext '$gap_ext'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	142 -N '$ambiguous_letter'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	143 -a \${GALAXY_SLOTS:-1}
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	144 #if $report.report_type != 'None'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	145 &&
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	146 samtools view -@ "\${GALAXY_SLOTS:-4}" -u aligned.sam \| samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o '$output_bam'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	147 #end if
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	148
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	149 #if $aligned_fastx.aligned_fastx_selector == '--fastx' and str($sequencing_type.sequencing_type_selector) == 'paired'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	150 #if str($sequencing_type.paired_type) != ''
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	151 &&
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	152 unmerge-paired-reads.sh
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	153 aligned.fast*
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	154 '$aligned_forward'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	155 '$aligned_reverse'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	156 #if $aligned_fastx.other
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	157 &&
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	158 unmerge-paired-reads.sh
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	159 unaligned.fast*
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	160 '$unaligned_forward'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	161 '$unaligned_reverse'
5 233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	162 #end if
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	163 #else
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	164 &&
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	165 mv aligned.fast* '$aligned_paired'
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	166 #if $aligned_fastx.other
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	167 &&
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	168 mv unaligned.fast* '$unaligned_paired'
5 233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	169 #end if
3 42509ccf8f59 Uploaded iuc parents: diff changeset	170 #end if
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	171 #end if
3 42509ccf8f59 Uploaded iuc parents: diff changeset	172 ]]>
42509ccf8f59 Uploaded iuc parents: diff changeset	173 </command>
42509ccf8f59 Uploaded iuc parents: diff changeset	174 <inputs>
42509ccf8f59 Uploaded iuc parents: diff changeset	175 <conditional name="sequencing_type">
42509ccf8f59 Uploaded iuc parents: diff changeset	176 <param name="sequencing_type_selector" type="select" label="Sequencing type">
42509ccf8f59 Uploaded iuc parents: diff changeset	177 <option value="not_paired">Reads are not paired</option>
42509ccf8f59 Uploaded iuc parents: diff changeset	178 <option value="paired">Reads are paired</option>
42509ccf8f59 Uploaded iuc parents: diff changeset	179 </param>
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	180 <when value="not_paired">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	181 <param argument="--reads" type="data" format="fasta,fastq" label="Querying sequences"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	182 </when>
3 42509ccf8f59 Uploaded iuc parents: diff changeset	183 <when value="paired">
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	184 <param name="forward_reads" type="data" format="fasta,fastq" label="Forward reads"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	185 <param name="reverse_reads" type="data" format="fasta,fastq" label="Reverse reads"/>
3 42509ccf8f59 Uploaded iuc parents: diff changeset	186 <param name="paired_type" type="select" display="radio" label="If one of the paired-end reads aligns and the other one does not">
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	187 <option value="">Leave the reads split between aligned and rejected files</option>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	188 <option value="--paired_in">Output both reads to aligned file (--paired_in)</option>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	189 <option value="--paired_out">Output both reads to rejected file (--paired_out)</option>
3 42509ccf8f59 Uploaded iuc parents: diff changeset	190 </param>
42509ccf8f59 Uploaded iuc parents: diff changeset	191 </when>
42509ccf8f59 Uploaded iuc parents: diff changeset	192 </conditional>
5 233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	193 <param name="strand_search" type="select" label="Which strands to search">
3 42509ccf8f59 Uploaded iuc parents: diff changeset	194 <option value="">Search both strands</option>
42509ccf8f59 Uploaded iuc parents: diff changeset	195 <option value="-F">Search only the forward strand (-F)</option>
42509ccf8f59 Uploaded iuc parents: diff changeset	196 <option value="-R">Search only the reverse-complementary strand (-R)</option>
42509ccf8f59 Uploaded iuc parents: diff changeset	197 </param>
42509ccf8f59 Uploaded iuc parents: diff changeset	198 <conditional name="databases_type">
42509ccf8f59 Uploaded iuc parents: diff changeset	199 <param name="databases_selector" type="select" label="Databases to query"
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	200 help="Public rRNA databases provided with SortMeRNA have been indexed. On the contrary, personal databases must be indexed each time SortMeRNA is launched. Please be patient, this may take some time depending on the size of the given database.">
5 233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	201 <option value="cached" selected="true">Public pre-indexed ribosomal databases</option>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	202 <option value="cached_to_index">Public ribosomal databases to index with non default parameters</option>
3 42509ccf8f59 Uploaded iuc parents: diff changeset	203 <option value="history">Databases from your history</option>
42509ccf8f59 Uploaded iuc parents: diff changeset	204 </param>
42509ccf8f59 Uploaded iuc parents: diff changeset	205 <when value="cached">
42509ccf8f59 Uploaded iuc parents: diff changeset	206 <param name="input_databases" label="rRNA databases" type="select" display="checkboxes" multiple="true">
42509ccf8f59 Uploaded iuc parents: diff changeset	207 <options from_data_table="rRNA_databases" />
42509ccf8f59 Uploaded iuc parents: diff changeset	208 <validator type="no_options" message="Select at least one database"/>
42509ccf8f59 Uploaded iuc parents: diff changeset	209 </param>
42509ccf8f59 Uploaded iuc parents: diff changeset	210 </when>
5 233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	211 <when value="cached_to_index">
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	212 <param name="input_databases" label="rRNA databases" type="select" display="checkboxes" multiple="true">
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	213 <options from_data_table="rRNA_databases" />
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	214 <validator type="no_options" message="Select at least one database"/>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	215 </param>
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	216 <expand macro="db_prep"/>
5 233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	217 </when>
3 42509ccf8f59 Uploaded iuc parents: diff changeset	218 <when value="history">
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	219 <param name="database_name" type="data" format="fasta" multiple="true" label="rRNA databases" help="Your databases will be indexed first, which may take up to several minutes."/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	220 <expand macro="db_prep"/>
3 42509ccf8f59 Uploaded iuc parents: diff changeset	221 </when>
42509ccf8f59 Uploaded iuc parents: diff changeset	222 </conditional>
42509ccf8f59 Uploaded iuc parents: diff changeset	223 <!-- Outputs -->
42509ccf8f59 Uploaded iuc parents: diff changeset	224 <conditional name="aligned_fastx">
5 233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	225 <param name="aligned_fastx_selector" type="select" label="Include aligned reads in FASTA/FASTQ format?">
3 42509ccf8f59 Uploaded iuc parents: diff changeset	226 <option value="--fastx">Yes (--fastx)</option>
42509ccf8f59 Uploaded iuc parents: diff changeset	227 <option value="">No</option>
42509ccf8f59 Uploaded iuc parents: diff changeset	228 </param>
42509ccf8f59 Uploaded iuc parents: diff changeset	229 <when value="--fastx">
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	230 <param argument="--other" type="boolean" truevalue="True" falsevalue="False" label="Include rejected reads file?"/>
3 42509ccf8f59 Uploaded iuc parents: diff changeset	231 </when>
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	232 <when value=""/>
3 42509ccf8f59 Uploaded iuc parents: diff changeset	233 </conditional>
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	234 <param argument="--log" type="boolean" checked="false" truevalue="--log" falsevalue="" label="Generate statistics file" help="Generates statistics for the rRNA content of reads, as well as rRNA subunit distribution">
3 42509ccf8f59 Uploaded iuc parents: diff changeset	235 </param>
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	236 <conditional name="report">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	237 <param name="report_type" type="select" label="Alignment report">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	238 <option value="None">Do not report alignments</option>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	239 <option value="best">Report best alignments per read reaching E-value</option>
5 233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	240 <option value="num_alignments">Report first alignements per read reaching E-value</option>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	241 </param>
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	242 <when value="None"/>
5 233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	243 <when value="best">
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	244 <expand macro="output_alignments"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	245 <conditional name="otu">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	246 <param name="otu_map" type="select" label="Pick OTUs?">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	247 <option value="True">Yes</option>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	248 <option value="False" selected="true">No</option>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	249 </param>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	250 <when value="True">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	251 <param argument="--id" type="float" value="0.97" label="Percentage id similarity threshold" help="The alignment must still pass the E-value threshold" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	252 <param argument="--coverage" type="float" value="0.97" label="Percentage query coverage threshold" help="The alignment must still pass the E-value threshold" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	253 <param name="de_novo_otu" type="boolean" truevalue="--de_novo_otu" falsevalue="" label="FASTA/FASTQ file for reads matching database below percentage id" help="--de_novo_otu" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	254 </when>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	255 <when value="False"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	256 </conditional>
5 233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	257 <conditional name="report_best">
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	258 <param argument="report_best_type" type="select" label="Number of searched alignments" help="Only the best alignment is reported (--best)">
5 233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	259 <option value="1" selected="true">Only one high-candidate reference sequence is searched for alignments (fast). The high-candidate sequences are determined heuristically using a LIS of seed matches)</option>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	260 <option value="other_value">A custom number of reference sequences are searched for alignments (speed decrease for high value)</option>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	261 </param>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	262 <when value="1">
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	263 <param name="report_best_min_lis" type="integer" min="0" max="100" value="2" label="Number of longest LIS an alignement needs to be searched" help="The alignements having the first INT longest LIS. LIS stands for Longest Increasing Subsequence, it is computed using seeds' positions to expand hits into longer matches prior to Smith-Waterman alignment. (--min_lis)"/>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	264 </when>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	265 <when value="other_value">
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	266 <param name="report_best_value" type="integer" min="2" max="100" value="2" label="Number of alignments to be made" help="Only the best one is reported. The computation speed decrease with high value"/>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	267 <param name="report_best_min_lis" type="integer" min="0" max="100" value="2" label="Number of longest LIS an alignement needs to be searched" help="The alignements having the first INT longest LIS. LIS stands for Longest Increasing Subsequence, it is computed using seeds' positions to expand hits into longer matches prior to Smith-Waterman alignment. (--min_lis)"/>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	268 </when>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	269 </conditional>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	270 </when>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	271 <when value="num_alignments">
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	272 <expand macro="output_alignments"/>
5 233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	273 <conditional name="report_num_alignments">
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	274 <param name="report_num_alignments_type" type="select" label="Number of output alignments" help="(--num_alignments)">
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	275 <option value="0">All alignments reaching the E-value threshold are reported (very slow, this option is not suggested for high similarity rRNA databases)</option>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	276 <option value="1" selected="true">The first alignment passing E-value threshold are reported (very fast, best choice if only filtering is needed)</option>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	277 <option value="other_value">A custom number of alignments are made and reported (speed decrease for high value)</option>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	278 </param>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	279 <when value="0" />
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	280 <when value="1" />
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	281 <when value="other_value">
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	282 <param name="report_num_alignments_value" type="integer" min="0" max="100" value="1" label="Number of alignments to be made and reported" help=""/>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	283 </when>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	284 </conditional>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	285 </when>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	286 </conditional>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	287 <param name="e_value" type="float" min="0" max="10" value="1" label="E-value threshold" help="(-e)"/>
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	288 <param argument="--match" type="integer" min="0" max="10" value="2" label="SW score for a match"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	289 <param argument="--mismatch" type="integer" min="-10" max="0" value="-3" label="SW penalty for a mismatch"/>
5 233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	290 <param name="gap_open" type="integer" min="0" max="10" value="5" label="SW penalty for introducing a gap" help="(--gap_open)"/>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	291 <param name="gap_ext" type="integer" min="0" max="10" value="2" label="SW penalty for extending a gap" help="(--gap_ext)"/>
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	292 <param name="ambiguous_letter" type="integer" min="-10" max="0" value="-3" label="SW penalty for ambiguous letters (N's)" help="(-N)"/>
3 42509ccf8f59 Uploaded iuc parents: diff changeset	293 </inputs>
42509ccf8f59 Uploaded iuc parents: diff changeset	294 <outputs>
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	295 <data name="output_fastx" format_source="reads" from_work_dir="aligned.dat" label="${tool.name} on ${on_string}: Aligned reads">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	296 <filter>aligned_fastx['aligned_fastx_selector'] != '' and sequencing_type['sequencing_type_selector'] != 'paired'</filter>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	297 </data>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	298 <data name="aligned_paired" format_source="forward_reads" label="${tool.name} on ${on_string}: Aligned reads">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	299 <filter>aligned_fastx['aligned_fastx_selector'] != '' and sequencing_type['sequencing_type_selector'] == 'paired' and sequencing_type['paired_type'] == ''</filter>
3 42509ccf8f59 Uploaded iuc parents: diff changeset	300 </data>
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	301 <data name="aligned_forward" format_source="forward_reads" label="${tool.name} on ${on_string}: Aligned forward reads">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	302 <filter>aligned_fastx['aligned_fastx_selector'] != '' and sequencing_type['sequencing_type_selector'] == 'paired' and sequencing_type['paired_type'] != ''</filter>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	303 </data>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	304 <data name="aligned_reverse" format_source="reverse_reads" label="${tool.name} on ${on_string}: Aligned reverse reads">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	305 <filter>aligned_fastx['aligned_fastx_selector'] != '' and sequencing_type['sequencing_type_selector'] == 'paired' and sequencing_type['paired_type'] != ''</filter>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	306 </data>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	307 <data name="output_other" format_source="reads" from_work_dir="unaligned.dat" label="${tool.name} on ${on_string}: Unaligned reads">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	308 <filter>aligned_fastx['aligned_fastx_selector'] != '' and aligned_fastx['other'] == True and sequencing_type['sequencing_type_selector'] != 'paired'</filter>
3 42509ccf8f59 Uploaded iuc parents: diff changeset	309 </data>
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	310 <data name="unaligned_paired" format_source="forward_reads" label="${tool.name} on ${on_string}: Unaligned reads">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	311 <filter>aligned_fastx['aligned_fastx_selector'] != '' and aligned_fastx['other'] == True and sequencing_type['sequencing_type_selector'] == 'paired' and sequencing_type['paired_type'] == ''</filter>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	312 </data>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	313 <data name="unaligned_forward" format_source="forward_reads" label="${tool.name} on ${on_string}: Unaligned forward reads">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	314 <filter>aligned_fastx['aligned_fastx_selector'] != '' and aligned_fastx['other'] == True and sequencing_type['sequencing_type_selector'] == 'paired' and sequencing_type['paired_type'] != ''</filter>
3 42509ccf8f59 Uploaded iuc parents: diff changeset	315 </data>
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	316 <data name="unaligned_reverse" format_source="reverse_reads" label="${tool.name} on ${on_string}: Unaligned reverse reads">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	317 <filter>aligned_fastx['aligned_fastx_selector'] != '' and aligned_fastx['other'] == True and sequencing_type['sequencing_type_selector'] == 'paired' and sequencing_type['paired_type'] != ''</filter>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	318 </data>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	319 <data name="output_bam" format="bam" label="${tool.name} on ${on_string}: Alignments">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	320 <filter>report['report_type'] != 'None'</filter>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	321 </data>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	322 <data name="output_blast" format="tabular" from_work_dir="aligned.blast" label="${tool.name} on ${on_string}: BLAST report">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	323 <filter>report['report_type'] != 'None' and report['blast']['blast_output'] == 'True'</filter>
3 42509ccf8f59 Uploaded iuc parents: diff changeset	324 <change_format>
7 bf2866308fbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 5a8ffc52b7076d8d4fbc9649703bb4c0155b726c rnateam parents: 6 diff changeset	325 <when input="aligned_blast.aligned_blast_format" value="0" format="txt" />
3 42509ccf8f59 Uploaded iuc parents: diff changeset	326 </change_format>
42509ccf8f59 Uploaded iuc parents: diff changeset	327 </data>
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	328 <data name="output_biom" format="txt" from_work_dir="aligned_otus.txt" label="${tool.name} on ${on_string}: OTU map">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	329 <filter>report['report_type'] != 'None' and report['report_type'] == 'best' and report['otu']['otu_map'] == 'True'</filter>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	330 </data>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	331 <data name="output_de_novo" format_source="reads" from_work_dir="aligned_denovo.dat" label="${tool.name} on ${on_string}: De novo reads matching database">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	332 <filter>report['report_type'] != 'None' and report['report_type'] == 'best' and report['otu']['otu_map'] == 'True' and report['otu']['de_novo_otu'] == True</filter>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	333 </data>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	334 <data name="output_log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="aligned.log">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	335 <filter>log == True</filter>
3 42509ccf8f59 Uploaded iuc parents: diff changeset	336 </data>
42509ccf8f59 Uploaded iuc parents: diff changeset	337 </outputs>
42509ccf8f59 Uploaded iuc parents: diff changeset	338 <tests>
42509ccf8f59 Uploaded iuc parents: diff changeset	339 <test>
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	340 <conditional name="sequencing_type">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	341 <param name="sequencing_type_selector" value="not_paired" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	342 <param name="reads" value="read_small.fastq" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	343 </conditional>
3 42509ccf8f59 Uploaded iuc parents: diff changeset	344 <param name="strand_search" value="" />
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	345 <conditional name="databases_type">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	346 <param name="databases_selector" value="history" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	347 <param name="database_name" value="ref_small.fasta" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	348 </conditional>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	349 <conditional name="aligned_fastx">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	350 <param name="aligned_fastx_selector" value="--fastx" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	351 <param name="other" value="True" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	352 </conditional>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	353 <param name="log" value="False" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	354 <conditional name="report">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	355 <param name="report_type" value="num_alignments" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	356 <param name="report_best_type" value="1" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	357 <param name="print_all_reads" value="False" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	358 <conditional name="blast">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	359 <param name="blast_output" value="True"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	360 <param name="blast_format" value="1 cigar qcov"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	361 </conditional>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	362 <conditional name="otu">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	363 <param name="otu_map" value="False"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	364 </conditional>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	365 </conditional>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	366 <param name="e_value" value="1"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	367 <param name="match" value="2"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	368 <param name="mismatch" value="-3" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	369 <param name="gap_open" value="5"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	370 <param name="gap_ext" value="2"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	371 <param name="ambiguous_letter" value="-3"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	372 <output name="output_fastx" file="test1_aligned.fastq" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	373 <output name="output_other" file="test1_other.fastq" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	374 <output name="output_bam" file="test1_bam.bam" compare="sim_size" delta="200" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	375 <output name="output_blast" file="test1_blast.tabular"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	376 </test>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	377 <test>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	378 <conditional name="sequencing_type">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	379 <param name="sequencing_type_selector" value="not_paired" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	380 <param name="reads" value="read_small.fasta" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	381 </conditional>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	382 <param name="strand_search" value="" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	383 <conditional name="databases_type">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	384 <param name="databases_selector" value="history" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	385 <param name="database_name" value="ref_small.fasta" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	386 </conditional>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	387 <conditional name="aligned_fastx">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	388 <param name="aligned_fastx_selector" value="--fastx" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	389 <param name="other" value="False" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	390 </conditional>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	391 <param name="log" value="True" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	392 <conditional name="report">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	393 <param name="report_type" value="None" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	394 </conditional>
7 bf2866308fbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 5a8ffc52b7076d8d4fbc9649703bb4c0155b726c rnateam parents: 6 diff changeset	395 <param name="e_value" value="1"/>
bf2866308fbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 5a8ffc52b7076d8d4fbc9649703bb4c0155b726c rnateam parents: 6 diff changeset	396 <param name="match" value="2"/>
bf2866308fbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 5a8ffc52b7076d8d4fbc9649703bb4c0155b726c rnateam parents: 6 diff changeset	397 <param name="mismatch" value="-3" />
bf2866308fbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 5a8ffc52b7076d8d4fbc9649703bb4c0155b726c rnateam parents: 6 diff changeset	398 <param name="gap_open" value="5"/>
bf2866308fbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 5a8ffc52b7076d8d4fbc9649703bb4c0155b726c rnateam parents: 6 diff changeset	399 <param name="gap_ext" value="2"/>
bf2866308fbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 5a8ffc52b7076d8d4fbc9649703bb4c0155b726c rnateam parents: 6 diff changeset	400 <param name="ambiguous_letter" value="-3"/>
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	401 <output name="output_fastx" file="test2_aligned.fasta" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	402 <output name="output_log" file="test2_log.txt" compare="sim_size" />
3 42509ccf8f59 Uploaded iuc parents: diff changeset	403 </test>
42509ccf8f59 Uploaded iuc parents: diff changeset	404 <test>
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	405 <conditional name="sequencing_type">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	406 <param name="sequencing_type_selector" value="paired" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	407 <param name="forward_reads" value="forward_reads.fastq" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	408 <param name="reverse_reads" value="reverse_reads.fastq" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	409 <param name="paired_type" value="--paired_in"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	410 </conditional>
3 42509ccf8f59 Uploaded iuc parents: diff changeset	411 <param name="strand_search" value="" />
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	412 <conditional name="databases_type">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	413 <param name="databases_selector" value="history" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	414 <param name="database_name" value="ref_small.fasta" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	415 <param name="seed_length" value="18" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	416 <param name="max_pos" value="100000"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	417 </conditional>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	418 <conditional name="aligned_fastx">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	419 <param name="aligned_fastx_selector" value="--fastx" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	420 <param name="other" value="True" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	421 </conditional>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	422 <param name="log" value="False" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	423 <conditional name="report">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	424 <param name="report_type" value="best" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	425 <param name="report_num_alignments_type" value="1"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	426 <param name="print_all_reads" value="False" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	427 <conditional name="blast">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	428 <param name="blast_output" value="False"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	429 </conditional>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	430 <conditional name="otu">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	431 <param name="otu_map" value="False"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	432 </conditional>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	433 </conditional>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	434 <param name="e_value" value="1"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	435 <param name="match" value="2"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	436 <param name="mismatch" value="-3" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	437 <param name="gap_open" value="5"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	438 <param name="gap_ext" value="2"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	439 <param name="ambiguous_letter" value="-3"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	440 <output name="aligned_forward" file="test3_aligned_forward.fastq" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	441 <output name="aligned_reverse" file="test3_aligned_reverse.fastq" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	442 <output name="unaligned_forward" file="test3_unaligned_forward.fastq" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	443 <output name="unaligned_reverse" file="test3_unaligned_reverse.fastq" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	444 <output name="output_bam" file="test3_bam.bam" compare="sim_size" delta="200" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	445 </test>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	446 <test>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	447 <conditional name="sequencing_type">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	448 <param name="sequencing_type_selector" value="not_paired" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	449 <param name="reads" value="test4_input.fasta" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	450 </conditional>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	451 <param name="strand_search" value="" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	452 <conditional name="databases_type">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	453 <param name="databases_selector" value="history" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	454 <param name="database_name" value="ref_small.fasta" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	455 <param name="seed_length" value="18" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	456 <param name="max_pos" value="100000"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	457 </conditional>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	458 <conditional name="aligned_fastx">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	459 <param name="aligned_fastx_selector" value="" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	460 </conditional>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	461 <param name="log" value="False" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	462 <conditional name="report">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	463 <param name="report_type" value="best" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	464 <param name="report_num_alignments_type" value="1"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	465 <param name="print_all_reads" value="False" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	466 <conditional name="blast">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	467 <param name="blast_output" value="False"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	468 </conditional>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	469 <conditional name="otu">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	470 <param name="otu_map" value="True"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	471 <param name="id" value="0.97"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	472 <param name="coverage" value="0.97" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	473 <param name="de_novo_otu" value="True"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	474 </conditional>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	475 </conditional>
7 bf2866308fbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 5a8ffc52b7076d8d4fbc9649703bb4c0155b726c rnateam parents: 6 diff changeset	476 <param name="e_value" value="1"/>
bf2866308fbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 5a8ffc52b7076d8d4fbc9649703bb4c0155b726c rnateam parents: 6 diff changeset	477 <param name="match" value="2"/>
bf2866308fbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 5a8ffc52b7076d8d4fbc9649703bb4c0155b726c rnateam parents: 6 diff changeset	478 <param name="mismatch" value="-3" />
bf2866308fbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 5a8ffc52b7076d8d4fbc9649703bb4c0155b726c rnateam parents: 6 diff changeset	479 <param name="gap_open" value="5"/>
bf2866308fbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 5a8ffc52b7076d8d4fbc9649703bb4c0155b726c rnateam parents: 6 diff changeset	480 <param name="gap_ext" value="2"/>
bf2866308fbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 5a8ffc52b7076d8d4fbc9649703bb4c0155b726c rnateam parents: 6 diff changeset	481 <param name="ambiguous_letter" value="-3"/>
12 67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	482 <output name="output_bam" file="test4_bam.bam" compare="sim_size" delta="200" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	483 <output name="output_biom" file="test4_biom.txt"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	484 <output name="output_de_novo" file="test4_de_novo.fasta"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	485 </test>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	486 <test>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	487 <conditional name="sequencing_type">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	488 <param name="sequencing_type_selector" value="paired" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	489 <param name="forward_reads" value="forward_reads.fasta" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	490 <param name="reverse_reads" value="reverse_reads.fasta" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	491 <param name="paired_type" value=""/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	492 </conditional>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	493 <param name="strand_search" value="" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	494 <conditional name="databases_type">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	495 <param name="databases_selector" value="history" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	496 <param name="database_name" value="ref_small.fasta" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	497 <param name="seed_length" value="18" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	498 <param name="max_pos" value="100000"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	499 </conditional>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	500 <conditional name="aligned_fastx">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	501 <param name="aligned_fastx_selector" value="--fastx" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	502 <param name="other" value="True" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	503 </conditional>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	504 <param name="log" value="False" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	505 <conditional name="report">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	506 <param name="report_type" value="best" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	507 <param name="report_num_alignments_type" value="1"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	508 <param name="print_all_reads" value="False" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	509 <conditional name="blast">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	510 <param name="blast_output" value="False"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	511 </conditional>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	512 <conditional name="otu">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	513 <param name="otu_map" value="False"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	514 </conditional>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	515 </conditional>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	516 <param name="e_value" value="1"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	517 <param name="match" value="2"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	518 <param name="mismatch" value="-3" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	519 <param name="gap_open" value="5"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	520 <param name="gap_ext" value="2"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	521 <param name="ambiguous_letter" value="-3"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	522 <output name="aligned_paired" file="test5_aligned.fasta" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	523 <output name="unaligned_paired" file="test5_unaligned.fasta" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	524 </test>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	525 <test>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	526 <conditional name="sequencing_type">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	527 <param name="sequencing_type_selector" value="paired" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	528 <param name="forward_reads" value="forward_reads.fasta" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	529 <param name="reverse_reads" value="reverse_reads.fasta" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	530 <param name="paired_type" value="--paired_out"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	531 </conditional>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	532 <param name="strand_search" value="" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	533 <conditional name="databases_type">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	534 <param name="databases_selector" value="history" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	535 <param name="database_name" value="ref_small.fasta" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	536 <param name="seed_length" value="18" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	537 <param name="max_pos" value="100000"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	538 </conditional>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	539 <conditional name="aligned_fastx">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	540 <param name="aligned_fastx_selector" value="--fastx" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	541 <param name="other" value="True" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	542 </conditional>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	543 <param name="log" value="False" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	544 <conditional name="report">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	545 <param name="report_type" value="best" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	546 <param name="report_num_alignments_type" value="1"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	547 <param name="print_all_reads" value="False" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	548 <conditional name="blast">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	549 <param name="blast_output" value="False"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	550 </conditional>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	551 <conditional name="otu">
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	552 <param name="otu_map" value="False"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	553 </conditional>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	554 </conditional>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	555 <param name="e_value" value="1"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	556 <param name="match" value="2"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	557 <param name="mismatch" value="-3" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	558 <param name="gap_open" value="5"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	559 <param name="gap_ext" value="2"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	560 <param name="ambiguous_letter" value="-3"/>
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	561 <output name="aligned_forward" file="test6_aligned_forward.fasta" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	562 <output name="aligned_reverse" file="test6_aligned_reverse.fasta" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	563 <output name="unaligned_forward" file="test6_unaligned_forward.fasta" />
67a87a218aa4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc rnateam parents: 11 diff changeset	564 <output name="unaligned_reverse" file="test6_unaligned_reverse.fasta" />
3 42509ccf8f59 Uploaded iuc parents: diff changeset	565 </test>
42509ccf8f59 Uploaded iuc parents: diff changeset	566 </tests>
42509ccf8f59 Uploaded iuc parents: diff changeset	567 <help>
42509ccf8f59 Uploaded iuc parents: diff changeset	568 <![CDATA[
42509ccf8f59 Uploaded iuc parents: diff changeset	569 What it does
42509ccf8f59 Uploaded iuc parents: diff changeset	570
42509ccf8f59 Uploaded iuc parents: diff changeset	571 SortMeRNA_ is a software designed to rapidly filter ribosomal RNA fragments
42509ccf8f59 Uploaded iuc parents: diff changeset	572 from metatransriptomic data produced by next-generation sequencers.
42509ccf8f59 Uploaded iuc parents: diff changeset	573 It is capable of handling large RNA databases and sorting out all fragments
42509ccf8f59 Uploaded iuc parents: diff changeset	574 matching to the database with high accuracy and specificity.
42509ccf8f59 Uploaded iuc parents: diff changeset	575
42509ccf8f59 Uploaded iuc parents: diff changeset	576 .. _SortMeRNA: http://bioinfo.lifl.fr/RNA/sortmerna/
42509ccf8f59 Uploaded iuc parents: diff changeset	577
42509ccf8f59 Uploaded iuc parents: diff changeset	578
42509ccf8f59 Uploaded iuc parents: diff changeset	579 Input
42509ccf8f59 Uploaded iuc parents: diff changeset	580
42509ccf8f59 Uploaded iuc parents: diff changeset	581 The input is one file of reads in FASTA or FASTQ format and any number of rRNA databases to search against.
42509ccf8f59 Uploaded iuc parents: diff changeset	582 If the user has two foward-reverse paired-sequencing reads files, they may use
42509ccf8f59 Uploaded iuc parents: diff changeset	583 the script "merge_paired_reads.sh" to interleave the reads into one file, preserving their order.
42509ccf8f59 Uploaded iuc parents: diff changeset	584
42509ccf8f59 Uploaded iuc parents: diff changeset	585 If the sequencing type for the reads is paired-ended, the user has two options under
42509ccf8f59 Uploaded iuc parents: diff changeset	586 "Sequencing type" to filter the reads and preserve their order in the file.
42509ccf8f59 Uploaded iuc parents: diff changeset	587 For a further example of each option, please refer to Section 4.2.3 in the `SortMeRNA User Manual`_.
42509ccf8f59 Uploaded iuc parents: diff changeset	588
42509ccf8f59 Uploaded iuc parents: diff changeset	589 .. _sortmerna user manual: http://bioinfo.lifl.fr/RNA/sortmerna/code/SortMeRNA-user-manual-v1.7.pdf
42509ccf8f59 Uploaded iuc parents: diff changeset	590
42509ccf8f59 Uploaded iuc parents: diff changeset	591
42509ccf8f59 Uploaded iuc parents: diff changeset	592 Output
42509ccf8f59 Uploaded iuc parents: diff changeset	593
42509ccf8f59 Uploaded iuc parents: diff changeset	594 The output will follow the same format (FASTA or FASTQ) as the reads. Optionally, a statistic file for the rRNA content of reads, as well as rRNA subunit distribution can be generated.
42509ccf8f59 Uploaded iuc parents: diff changeset	595
42509ccf8f59 Uploaded iuc parents: diff changeset	596
42509ccf8f59 Uploaded iuc parents: diff changeset	597 rRNA databases
42509ccf8f59 Uploaded iuc parents: diff changeset	598
42509ccf8f59 Uploaded iuc parents: diff changeset	599 SortMeRNA is distributed with 8 representative rRNA databases, which were
42509ccf8f59 Uploaded iuc parents: diff changeset	600 all constructed from the SILVA SSU,LSU (version 111) and the RFAM 5/5.8S
42509ccf8f59 Uploaded iuc parents: diff changeset	601 (version 11.0) databases using the tool UCLUST.
42509ccf8f59 Uploaded iuc parents: diff changeset	602
42509ccf8f59 Uploaded iuc parents: diff changeset	603 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
42509ccf8f59 Uploaded iuc parents: diff changeset	604 \| Representative database \| id % \| average id% \| # seq (clustered) \| Origin \| # seq (original) \|
42509ccf8f59 Uploaded iuc parents: diff changeset	605 +==========================+======+=============+===================+========================+===================+
42509ccf8f59 Uploaded iuc parents: diff changeset	606 \| SILVA 16S bacteria \| 85 \| 91.6 \| 8174 \| SILVA SSU Ref NR v.111 \| 244077 \|
42509ccf8f59 Uploaded iuc parents: diff changeset	607 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
42509ccf8f59 Uploaded iuc parents: diff changeset	608 \| SILVA 16S archaea \| 95 \| 96.7 \| 3845 \| SILVA SSU Ref NR v.111 \| 10919 \|
42509ccf8f59 Uploaded iuc parents: diff changeset	609 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
42509ccf8f59 Uploaded iuc parents: diff changeset	610 \| SILVA 18S eukarya \| 95 \| 96.7 \| 4512 \| SILVA SSU Ref NR v.111 \| 31862 \|
42509ccf8f59 Uploaded iuc parents: diff changeset	611 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
42509ccf8f59 Uploaded iuc parents: diff changeset	612 \| SILVA 23S bacteria \| 98 \| 99.4 \| 3055 \| SILVA LSU Ref v.111 \| 19580 \|
42509ccf8f59 Uploaded iuc parents: diff changeset	613 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
42509ccf8f59 Uploaded iuc parents: diff changeset	614 \| SILVA 23s archaea \| 98 \| 99.5 \| 164 \| SILVA LSU Ref v.111 \| 405 \|
42509ccf8f59 Uploaded iuc parents: diff changeset	615 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
42509ccf8f59 Uploaded iuc parents: diff changeset	616 \| SILVA 28S eukarya \| 98 \| 99.1 \| 4578 \| SILVA LSU Ref v.111 \| 9321 \|
42509ccf8f59 Uploaded iuc parents: diff changeset	617 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
42509ccf8f59 Uploaded iuc parents: diff changeset	618 \| Rfam 5S archaea/bacteria \| 98 \| 99.2 \| 59513 \| RFAM \| 116760 \|
42509ccf8f59 Uploaded iuc parents: diff changeset	619 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
42509ccf8f59 Uploaded iuc parents: diff changeset	620 \| Rfam 5.8S eukarya \| 98 \| 98.9 \| 13034 \| RFAM \| 225185 \|
42509ccf8f59 Uploaded iuc parents: diff changeset	621 +--------------------------+------+-------------+-------------------+------------------------+-------------------+
42509ccf8f59 Uploaded iuc parents: diff changeset	622
42509ccf8f59 Uploaded iuc parents: diff changeset	623 id %: members of the cluster must have identity at least 'id %' identity with the representative sequence
42509ccf8f59 Uploaded iuc parents: diff changeset	624
42509ccf8f59 Uploaded iuc parents: diff changeset	625 average id %: average identity of a cluster member to the representative sequence
42509ccf8f59 Uploaded iuc parents: diff changeset	626
42509ccf8f59 Uploaded iuc parents: diff changeset	627 The user may also choose to use their own rRNA databases.
42509ccf8f59 Uploaded iuc parents: diff changeset	628
42509ccf8f59 Uploaded iuc parents: diff changeset	629 .. class:: warningmark
42509ccf8f59 Uploaded iuc parents: diff changeset	630
5 233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	631 Note that your personal databases are indexed each time. The public ribosomal
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	632 databases are indexed when added, but they can be re-indexed with non-default indexing
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	633 parameters. The indexing may take some time depending on the size of the given database.
233da82dc31c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 4febb4056eb7b379edc0f3e7719a50e575a749c8 rnateam parents: 4 diff changeset	634
3 42509ccf8f59 Uploaded iuc parents: diff changeset	635 ]]>
42509ccf8f59 Uploaded iuc parents: diff changeset	636 </help>
42509ccf8f59 Uploaded iuc parents: diff changeset	637
42509ccf8f59 Uploaded iuc parents: diff changeset	638 <citations>
42509ccf8f59 Uploaded iuc parents: diff changeset	639 <citation type="doi">10.1093/bioinformatics/bts611</citation>
42509ccf8f59 Uploaded iuc parents: diff changeset	640 <citation type="doi">10.1093/nar/gks1219</citation>
42509ccf8f59 Uploaded iuc parents: diff changeset	641 <citation type="doi">10.1093/nar/gks1005</citation>
42509ccf8f59 Uploaded iuc parents: diff changeset	642 <citation type="doi">10.1093/bioinformatics/btq461</citation>
42509ccf8f59 Uploaded iuc parents: diff changeset	643 <citation type="doi">10.1038/nbt.2198</citation>
42509ccf8f59 Uploaded iuc parents: diff changeset	644 </citations>
42509ccf8f59 Uploaded iuc parents: diff changeset	645 </tool>

Mercurial > repos > rnateam > sortmerna

annotate sortmerna.xml @ 12:67a87a218aa4 draft default tip