rgrnastar: macros.xml annotate

annotate macros.xml @ 32:4746de55986e draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256

author	iuc
date	Sat, 31 May 2025 19:51:43 +0000
parents	9b7a86a83fce
children

rev	line source
4 13dba3e91459 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: diff changeset	1 <macros>
25 69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	2 <!-- REMEMBER to bump the version of @IDX_VERSION_SUFFIX@
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	3 whenever you make changes to the @TOOL_VERSION@ token!
16 dd0baa73558d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e" iuc parents: 15 diff changeset	4 The data manager uses a symlink to this macro file to keep the STAR and
25 69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	5 the index versions in sync, but you should manually update @IDX_VERSION_SUFFIX@ -->
11 de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	6 <!-- STAR version to be used -->
32 4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	7 <token name="@TOOL_VERSION@">2.7.11b</token>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	8 <token name="@VERSION_SUFFIX@">0</token>
25 69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	9 <token name="@PROFILE@">21.01</token>
11 de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	10 <!-- STAR index version compatible with this version of STAR
de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	11 This is the STAR version that introduced the index structure expected
de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	12 by the current version.
de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	13 It can be found for any specific version of STAR with:
de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	14 STAR -h \| grep versionGenome
de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	15 or by looking for the versionGenome parameter in source/parametersDefault
de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	16 of STAR's source code -->
17 2a75b3cde55e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 16 diff changeset	17 <token name="@IDX_VERSION@">2.7.4a</token>
31 9b7a86a83fce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 57d05675396f0b44265fb4dbc8f9f891c6073219 iuc parents: 30 diff changeset	18 <token name="@IDX_VERSION_SUFFIX@">3</token>
17 2a75b3cde55e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 16 diff changeset	19 <token name="@IDX_DATA_TABLE@">rnastar_index2x_versioned</token>
4 13dba3e91459 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: diff changeset	20 <xml name="requirements">
13dba3e91459 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: diff changeset	21 <requirements>
25 69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	22 <requirement type="package" version="@TOOL_VERSION@">star</requirement>
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	23 <requirement type="package" version="1.18">samtools</requirement>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	24 <requirement type="package" version="1.13">gzip</requirement>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	25 <yield/>
4 13dba3e91459 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: diff changeset	26 </requirements>
13dba3e91459 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: diff changeset	27 </xml>
18 c5fec2edd835 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9c34fd08b619a09028707a52c868d9be1ca02a6b" iuc parents: 17 diff changeset	28 <xml name="edam">
c5fec2edd835 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9c34fd08b619a09028707a52c868d9be1ca02a6b" iuc parents: 17 diff changeset	29 <edam_topics>
c5fec2edd835 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9c34fd08b619a09028707a52c868d9be1ca02a6b" iuc parents: 17 diff changeset	30 <edam_topic>topic_3170</edam_topic>
c5fec2edd835 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9c34fd08b619a09028707a52c868d9be1ca02a6b" iuc parents: 17 diff changeset	31 <edam_topic>topic_3308</edam_topic>
c5fec2edd835 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9c34fd08b619a09028707a52c868d9be1ca02a6b" iuc parents: 17 diff changeset	32 </edam_topics>
c5fec2edd835 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9c34fd08b619a09028707a52c868d9be1ca02a6b" iuc parents: 17 diff changeset	33 <edam_operations>
c5fec2edd835 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9c34fd08b619a09028707a52c868d9be1ca02a6b" iuc parents: 17 diff changeset	34 <edam_operation>operation_0292</edam_operation>
c5fec2edd835 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9c34fd08b619a09028707a52c868d9be1ca02a6b" iuc parents: 17 diff changeset	35 </edam_operations>
c5fec2edd835 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9c34fd08b619a09028707a52c868d9be1ca02a6b" iuc parents: 17 diff changeset	36 </xml>
13 4e4631631f40 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2911002ccd79fe062f6346ee5699ea262f92f04f" iuc parents: 12 diff changeset	37 <xml name="index_selection" token_with_gene_model="0">
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	38 <param argument="--genomeDir" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
17 2a75b3cde55e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 16 diff changeset	39 <options from_data_table="@IDX_DATA_TABLE@">
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	40 <filter type="static_value" column="4" value="@WITH_GENE_MODEL@"/>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	41 <filter type="static_value" column="5" value="@IDX_VERSION@"/>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	42 <filter type="sort_by" column="2"/>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	43 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
11 de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	44 </options>
de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	45 </param>
de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	46 </xml>
4 13dba3e91459 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: diff changeset	47 <token name="@FASTQ_GZ_OPTION@">
13dba3e91459 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: diff changeset	48 --readFilesCommand zcat
13dba3e91459 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: diff changeset	49 </token>
13dba3e91459 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: diff changeset	50 <xml name="citations">
13dba3e91459 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: diff changeset	51 <citations>
13dba3e91459 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: diff changeset	52 <citation type="doi">10.1093/bioinformatics/bts635</citation>
13dba3e91459 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: diff changeset	53 </citations>
13dba3e91459 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: diff changeset	54 </xml>
25 69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	55 <xml name="SJDBOPTIONS">
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	56 <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="false" help="Exon junction information for mapping splices"/>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	57 <param argument="--sjdbGTFfeatureExon" type="text" value="exon" label="Elements to use from the gene model to use for splice junctions" help="By default and for almost all cases: 'exon', referring to finding junctions at the RNA splice sites. This can optionally be changed to allow splicing at other levels, such as 'gene', 'transcript', 'CDS'."/>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	58 <param argument="--sjdbOverhang" type="integer" min="1" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1"/>
4 13dba3e91459 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: diff changeset	59 </xml>
9 d397a5703ed8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 8 diff changeset	60 <xml name="dbKeyActions">
d397a5703ed8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 8 diff changeset	61 <actions>
26 426c1546c6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17 iuc parents: 25 diff changeset	62 <expand macro="dbKeyAction"/>
9 d397a5703ed8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 8 diff changeset	63 </actions>
d397a5703ed8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 8 diff changeset	64 </xml>
26 426c1546c6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17 iuc parents: 25 diff changeset	65 <xml name="dbKeyAction">
426c1546c6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17 iuc parents: 25 diff changeset	66 <conditional name="refGenomeSource.geneSource">
426c1546c6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17 iuc parents: 25 diff changeset	67 <when value="indexed">
426c1546c6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17 iuc parents: 25 diff changeset	68 <action type="metadata" name="dbkey">
426c1546c6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17 iuc parents: 25 diff changeset	69 <option type="from_data_table" name="@IDX_DATA_TABLE@" column="1" offset="0">
426c1546c6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17 iuc parents: 25 diff changeset	70 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
426c1546c6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17 iuc parents: 25 diff changeset	71 <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
426c1546c6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17 iuc parents: 25 diff changeset	72 </option>
426c1546c6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17 iuc parents: 25 diff changeset	73 </action>
426c1546c6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17 iuc parents: 25 diff changeset	74 </when>
426c1546c6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17 iuc parents: 25 diff changeset	75 <when value="history">
426c1546c6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17 iuc parents: 25 diff changeset	76 <action type="metadata" name="dbkey">
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	77 <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey"/>
26 426c1546c6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17 iuc parents: 25 diff changeset	78 </action>
426c1546c6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17 iuc parents: 25 diff changeset	79 </when>
426c1546c6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17 iuc parents: 25 diff changeset	80 </conditional>
426c1546c6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17 iuc parents: 25 diff changeset	81 </xml>
11 de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	82 <token name="@TEMPINDEX@"><![CDATA[
de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	83 ## Create temporary index for custom reference
de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	84 #if str($refGenomeSource.geneSource) == 'history':
25 69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	85 #if $refGenomeSource.genomeFastaFiles.ext == "fasta"
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	86 ln -s '$refGenomeSource.genomeFastaFiles' refgenome.fa &&
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	87 #else
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	88 gunzip -c '$refGenomeSource.genomeFastaFiles' > refgenome.fa &&
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	89 #end if
11 de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	90 mkdir -p tempstargenomedir &&
de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	91 STAR
de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	92 --runMode genomeGenerate
de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	93 --genomeDir 'tempstargenomedir'
25 69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	94 --genomeFastaFiles refgenome.fa
11 de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	95 ## Handle difference between indices with/without annotations
17 2a75b3cde55e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 16 diff changeset	96 #if 'GTFconditional' in $refGenomeSource:
2a75b3cde55e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 16 diff changeset	97 ## GTFconditional exists only in STAR, but not STARsolo
2a75b3cde55e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 16 diff changeset	98 #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf':
2a75b3cde55e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 16 diff changeset	99 --sjdbOverhang '${refGenomeSource.GTFconditional.sjdbOverhang}'
2a75b3cde55e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 16 diff changeset	100 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
29 e416daaccd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32 iuc parents: 28 diff changeset	101 --sjdbGTFfeatureExon '${refGenomeSource.GTFconditional.sjdbGTFfeatureExon}'
17 2a75b3cde55e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 16 diff changeset	102 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
2a75b3cde55e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 16 diff changeset	103 --sjdbGTFtagExonParentTranscript Parent
2a75b3cde55e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 16 diff changeset	104 #end if
2a75b3cde55e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 16 diff changeset	105 #end if
2a75b3cde55e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 16 diff changeset	106 #else:
29 e416daaccd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32 iuc parents: 28 diff changeset	107 ## ref genome selection is less complex for STARsolo because
17 2a75b3cde55e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 16 diff changeset	108 ## with-gtf is mandatory there
2a75b3cde55e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 16 diff changeset	109 --sjdbOverhang '${refGenomeSource.sjdbOverhang}'
2a75b3cde55e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 16 diff changeset	110 --sjdbGTFfile '${refGenomeSource.sjdbGTFfile}'
29 e416daaccd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32 iuc parents: 28 diff changeset	111 --sjdbGTFfeatureExon '${refGenomeSource.sjdbGTFfeatureExon}'
17 2a75b3cde55e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 16 diff changeset	112 #if str($refGenomeSource.sjdbGTFfile.ext) == 'gff3':
11 de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	113 --sjdbGTFtagExonParentTranscript Parent
de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	114 #end if
de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	115 #end if
de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	116 #if str($refGenomeSource.genomeSAindexNbases):
de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	117 --genomeSAindexNbases ${refGenomeSource.genomeSAindexNbases}
de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	118 #end if
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	119 ## Diploid mode
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	120 #if 'diploidconditional' in $refGenomeSource:
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	121 #if str($refGenomeSource.diploidconditional.diploid) == 'Yes':
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	122 --genomeTransformVCF '${refGenomeSource.diploidconditional.genomeTransformVCF}'
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	123 --genomeTransformType Diploid
32 4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	124 #end if
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	125 #end if
11 de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	126 --runThreadN \${GALAXY_SLOTS:-4}
25 69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	127 ## in bytes
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	128 --limitGenomeGenerateRAM \$((\${GALAXY_MEMORY_MB:-31000} * 1000000))
11 de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	129 &&
de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	130 #end if
de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	131 ]]></token>
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	132 <token name="@REFGENOMEHANDLING@"><![CDATA[
11 de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	133 --runThreadN \${GALAXY_SLOTS:-4}
de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	134 --genomeLoad NoSharedMemory
de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	135 --genomeDir
de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	136 #if str($refGenomeSource.geneSource) == 'history':
de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	137 tempstargenomedir
de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	138 #else:
de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	139 '${refGenomeSource.GTFconditional.genomeDir.fields.path}'
de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	140 ## Handle difference between indices with/without annotations
25 69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	141 #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf-with-gtf':
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	142 --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	143 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
29 e416daaccd32 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32 iuc parents: 28 diff changeset	144 --sjdbGTFfeatureExon '${refGenomeSource.GTFconditional.sjdbGTFfeatureExon}'
25 69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	145 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	146 --sjdbGTFtagExonParentTranscript Parent
11 de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	147 #end if
de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	148 #end if
25 69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	149 #end if
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	150 ]]></token>
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	151 <token name="@READSHANDLING@"><![CDATA[
19 f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	152 ## Check that the input pairs are of the same type
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	153 ## otherwise STARsolo will run for a long time and then error out.
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	154 ## We consume either repeats of two inputs R1 + R2
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	155 ## or a collection of paired reads.
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	156 #if str($sc.input_types.use) == "repeat":
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	157 #set $reads1 = []
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	158 #set $reads2 = []
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	159 #for $r1, $r2 in zip($sc.input_types.input1, $sc.input_types.input2):
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	160 #assert $r1.datatype == $r2.datatype
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	161 #silent $reads1.append(str($r1))
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	162 #silent $reads2.append(str($r2))
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	163 #end for
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	164 #set $reads1 = ','.join($reads1)
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	165 #set $reads2 = ','.join($reads2)
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	166 #elif str($sc.input_types.use) == "list_paired":
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	167 #set $r1 = $sc.input_types.input_collection.forward
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	168 #set $r2 = $sc.input_types.input_collection.reverse
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	169 #set $reads1 = $r1
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	170 #set $reads2 = $r2
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	171 #end if
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	172 ## cDNA sequence(s) [R2] always go first, then barcode(s) [R1]
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	173 ## see: Section 3.2 of STAR manual for multiple inputs, and Section 13 for STARsolo inputs
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	174 --readFilesIn $reads2 $reads1
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	175 --soloCBmatchWLtype $sc.soloCBmatchWLtype
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	176 #if $r1.is_of_type('fastq.gz', 'fastqsanger.gz'):
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	177 @FASTQ_GZ_OPTION@
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	178 #end if
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	179 ]]></token>
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	180 <token name="@LIMITS@"><![CDATA[
25 69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	181 --limitOutSJoneRead $getVar('algo.params.junction_limits.limitOutSJoneRead', $getVar('solo.junction_limits.limitOutSJoneRead', 1000))
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	182 --limitOutSJcollapsed $getVar('algo.params.junction_limits.limitOutSJcollapsed', $getVar('solo.junction_limits.limitOutSJcollapsed', 1000000))
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	183 --limitSjdbInsertNsj $getVar('algo.params.junction_limits.limitSjdbInsertNsj', $getVar('solo.junction_limits.limitSjdbInsertNsj', 1000000))
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	184 ]]></token>
17 2a75b3cde55e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 16 diff changeset	185 <xml name="ref_selection">
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	186 <param argument="--genomeFastaFiles" type="data" format="fasta,fasta.gz" label="Select a reference genome"/>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	187 <param argument="--genomeSAindexNbases" type="integer" min="2" max="16" value="14" label="Length of the SA pre-indexing string" help="Typically between 10 and 15. Longer strings will use much more memory, but allow faster searches. For small genomes, the parameter --genomeSAindexNbases must be scaled down to min(14, log2(GenomeLength)/2 - 1)"/>
17 2a75b3cde55e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 16 diff changeset	188 </xml>
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	189 <xml name="stdio">
11 de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	190 <stdio>
de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	191 <regex match="FATAL error" source="both" level="fatal"/>
de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	192 <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/>
de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	193 <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/>
de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	194 <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/>
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	195 <yield/>
11 de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	196 </stdio>
de5a55bd9112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7edce75096aed3a1aac91d22e86a2739a53cb245 iuc parents: 9 diff changeset	197 </xml>
19 f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	198 <xml name="input_selection">
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	199 <conditional name="input_types">
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	200 <param name="use" type="select" label="Input Type">
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	201 <option value="repeat">Separate barcode and cDNA reads</option>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	202 <option value="list_paired">Paired collection of barcode and cDNA reads</option>
19 f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	203 </param>
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	204 <when value="repeat">
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	205 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" multiple="true" label="RNA-Seq FASTQ/FASTA file, Barcode reads"/>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	206 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input2" type="data" multiple="true" label="RNA-Seq FASTQ/FASTA file, cDNA reads"/>
19 f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	207 </when>
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	208 <when value="list_paired">
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	209 <param name="input_collection" collection_type="paired" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="Collection of Pairs"/>
19 f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	210 </when>
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	211 </conditional>
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	212 </xml>
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	213 <xml name="input_selection_smart_seq">
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	214 <conditional name="input_types_smart_seq">
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	215 <param name="use" type="select" label="Input Type">
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	216 <option value="list_single_end">Single-end FASTQ collection</option>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	217 <option value="list_paired_end">Paired FASTQ collection</option>
19 f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	218 </param>
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	219 <when value="list_single_end">
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	220 <param name="single_end_collection" collection_type="list" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="List of single-end FASTQ files"/>
19 f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	221 </when>
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	222 <when value="list_paired_end">
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	223 <param name="paired_end_collection" collection_type="list:paired" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="List of paired-end FASTQ files"/>
19 f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	224 </when>
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	225 </conditional>
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	226 </xml>
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	227 <xml name="umidedup_options">
26 426c1546c6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17 iuc parents: 25 diff changeset	228 <option value="1MM_All" selected="true">Collapse all UMIs with 1 mismatch distance to each other (1MM_All)</option>
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	229 <option value="1MM_Directional_UMItools">Directional method from the UMI-tool</option>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	230 <option value="1MM_Directional">Directional with stringent UMI deduplication</option>
19 f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	231 </xml>
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	232 <xml name="anchor_types">
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	233 <option value="0">Read start</option>
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	234 <option value="1">Read end</option>
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	235 <option value="2">Adapter start</option>
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	236 <option value="3">Adapter end</option>
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	237 </xml>
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	238 <xml name="cb_match_wl_common">
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	239 <option value="Exact">Exact</option>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	240 <option value="1MM">Single match (1MM)</option>
19 f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	241 </xml>
f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	242 <xml name="cb_match_wl_cellranger">
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	243 <option value="1MM_multi" selected="true">Multiple matches (CellRanger 2, 1MM_multi)</option>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	244 <option value="1MM_multi_pseudocounts">Multiple matches (CellRanger 3, 1MM_multi_pseudocounts)</option>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	245 <option value="1MM_multi_Nbase_pseudocounts">Multimatching to WL is allowed for CBs with N-bases (CellRanger 3, 1MM_multi_Nbase_pseudocounts)</option>
20 e1d0d6d87123 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 19 diff changeset	246 </xml>
e1d0d6d87123 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 19 diff changeset	247 <xml name="solo_adapter_params">
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	248 <param argument="--soloAdapterSequence" type="text" value="-" label="Adapter sequence to anchor barcodes.">
20 e1d0d6d87123 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 19 diff changeset	249 <sanitizer>
e1d0d6d87123 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 19 diff changeset	250 <valid initial="string.digits">
e1d0d6d87123 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 19 diff changeset	251 <add value="-"/>
e1d0d6d87123 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 19 diff changeset	252 <add value="A"/>
e1d0d6d87123 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 19 diff changeset	253 <add value="T"/>
e1d0d6d87123 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 19 diff changeset	254 <add value="C"/>
e1d0d6d87123 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 19 diff changeset	255 <add value="G"/>
e1d0d6d87123 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 19 diff changeset	256 <add value="N"/>
e1d0d6d87123 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 19 diff changeset	257 </valid>
e1d0d6d87123 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 19 diff changeset	258 </sanitizer>
e1d0d6d87123 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 19 diff changeset	259 </param>
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	260 <param argument="--soloAdapterMismatchesNmax" type="integer" min="1" value="1" label="Maximum number of mismatches allowed in adapter sequence"/>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	261 <param argument="--clipAdapterType" type="select">
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	262 <option value="Hamming" selected="true">Adapter clipping based on Hamming distance</option>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	263 <option value="CellRanger4">5p and 3p adapter clipping similar to CellRanger4</option>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	264 <option value="None">No adapter clipping</option>
20 e1d0d6d87123 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 19 diff changeset	265 </param>
19 f8fd5680fbd3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 18 diff changeset	266 </xml>
25 69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	267 <xml name="common_SAM_attributes">
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	268 <option value="NH" selected="true">NH (number of reported alignments/hits for the read)</option>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	269 <option value="HI" selected="true">HI (query hit index)</option>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	270 <option value="AS" selected="true">AS (local alignment score)</option>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	271 <option value="nM" selected="true">nM (number of mismatches per (paired) alignment)</option>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	272 <option value="NM">NM (edit distance of the aligned read to the reference)</option>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	273 <option value="MD">MD (string for mismatching positions)</option>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	274 <option value="jM">jM (intron motifs for all junctions)</option>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	275 <option value="jI">jI (1-based start and end of introns for all junctions)</option>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	276 </xml>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	277 <xml name="limits">
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	278 <section name="junction_limits" title="Junction Limits" expanded="false">
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	279 <param argument="--limitOutSJoneRead" type="integer" min="1" value="1000" label="Maximum number of junctions for one read (including all multimappers)"/>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	280 <param argument="--limitOutSJcollapsed" type="integer" min="1" value="1000000" label="Maximum number of collapsed junctions"/>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	281 <param argument="--limitSjdbInsertNsj" type="integer" min="0" value="1000000" label="Maximum number of inserts to be inserted into the genome on the fly."/>
25 69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	282 </section>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	283 </xml>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	284 <xml name="outCountActions">
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	285 <actions>
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	286 <action name="column_names" type="metadata" default="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand"/>
26 426c1546c6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17 iuc parents: 25 diff changeset	287 <expand macro="dbKeyAction"/>
25 69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	288 </actions>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	289 </xml>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	290 <xml name="outWig">
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	291 <conditional name="outWig">
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	292 <param name="outWigType" type="select" label="Compute coverage">
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	293 <option value="None">No coverage</option>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	294 <option value="bedGraph">Yes in bedgraph format</option>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	295 <option value="wiggle">Yes in wiggle format</option>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	296 </param>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	297 <when value="None">
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	298 <!-- This is necessary for the filtering of output -->
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	299 <param name="outWigStrand" type="hidden" value="false"/>
25 69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	300 </when>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	301 <when value="bedGraph">
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	302 <expand macro="outWigParams"/>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	303 </when>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	304 <when value="wiggle">
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	305 <expand macro="outWigParams"/>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	306 </when>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	307 </conditional>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	308 </xml>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	309 <xml name="outWigParams">
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	310 <param name="outWigTypeSecondWord" type="select" label="Input for coverage">
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	311 <option value="">Default (everything that mapped)</option>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	312 <option value="read_5p">signal from only 5’ of the 1st read</option>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	313 <option value="read2">signal from only 2nd read</option>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	314 </param>
28 9bf9c35dc70c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 7474e67190d0dcf2bd54c6b3cbfa30e54134c8a0 iuc parents: 27 diff changeset	315 <param argument="--outWigStrand" type="boolean" truevalue="Stranded" falsevalue="Unstranded" checked="true" label="Generate a coverage for each strand (stranded coverage)"/>
25 69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	316 <param argument="--outWigReferencesPrefix" type="text" value="-" label="prefix matching reference name" help="For example, set 'chr' if you mapped on an ensembl genome but you want to display on UCSC"/>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	317 <param argument="--outWigNorm" type="boolean" truevalue="RPM" falsevalue="None" checked="true" label="Normalize coverage to million of mapped reads (RPM)"/>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	318 </xml>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	319 <token name="@OUTWIG@"><![CDATA[
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	320 #if str($outWig.outWigType) != 'None':
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	321 --outWigType '$outWig.outWigType' '$outWig.outWigTypeSecondWord'
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	322 --outWigStrand '$outWig.outWigStrand'
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	323 --outWigReferencesPrefix '$outWig.outWigReferencesPrefix'
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	324 --outWigNorm '$outWig.outWigNorm'
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	325 #end if
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	326 ]]></token>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	327 <token name="@OUTWIGOUTPUTS@"><![CDATA[
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	328 #if str($outWig.outWigType) == "bedGraph":
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	329 && mv Signal.Unique.str1.out.bg Signal.Unique.str1.out
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	330 && mv Signal.UniqueMultiple.str1.out.bg Signal.UniqueMultiple.str1.out
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	331 #if str($outWig.outWigStrand) == "Stranded":
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	332 && mv Signal.Unique.str2.out.bg Signal.Unique.str2.out
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	333 && mv Signal.UniqueMultiple.str2.out.bg Signal.UniqueMultiple.str2.out
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	334 #end if
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	335 #elif str($outWig.outWigType) == "wiggle":
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	336 && mv Signal.Unique.str1.out.wig Signal.Unique.str1.out
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	337 && mv Signal.UniqueMultiple.str1.out.wig Signal.UniqueMultiple.str1.out
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	338 #if str($outWig.outWigStrand) == "Stranded":
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	339 && mv Signal.Unique.str2.out.wig Signal.Unique.str2.out
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	340 && mv Signal.UniqueMultiple.str2.out.wig Signal.UniqueMultiple.str2.out
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	341 #end if
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	342 #end if
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	343 ]]></token>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	344 <xml name="outWigOutputs">
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	345 <data format="bedgraph" name="signal_unique_str1" label="${tool.name} on ${on_string}: Coverage Uniquely mapped strand 1" from_work_dir="Signal.Unique.str1.out">
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	346 <filter>outWig['outWigType'] != "None"</filter>
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	347 <expand macro="dbKeyActions"/>
25 69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	348 <change_format>
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	349 <when input="outWig.outWigType" value="wiggle" format="wig"/>
25 69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	350 </change_format>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	351 </data>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	352 <data format="bedgraph" name="signal_uniquemultiple_str1" label="${tool.name} on ${on_string}: Coverage Uniquely + Multiple mapped strand 1" from_work_dir="Signal.UniqueMultiple.str1.out">
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	353 <filter>outWig['outWigType'] != "None"</filter>
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	354 <expand macro="dbKeyActions"/>
25 69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	355 <change_format>
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	356 <when input="outWig.outWigType" value="wiggle" format="wig"/>
25 69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	357 </change_format>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	358 </data>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	359 <data format="bedgraph" name="signal_unique_str2" label="${tool.name} on ${on_string}: Coverage Uniquely mapped strand 2" from_work_dir="Signal.Unique.str2.out">
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	360 <filter>outWig['outWigType'] != "None" and outWig['outWigStrand']</filter>
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	361 <expand macro="dbKeyActions"/>
25 69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	362 <change_format>
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	363 <when input="outWig.outWigType" value="wiggle" format="wig"/>
25 69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	364 </change_format>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	365 </data>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	366 <data format="bedgraph" name="signal_uniquemultiple_str2" label="${tool.name} on ${on_string}: Coverage Uniquely + Multiple mapped strand 2" from_work_dir="Signal.UniqueMultiple.str2.out">
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	367 <filter>outWig['outWigType'] != "None" and outWig['outWigStrand']</filter>
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	368 <expand macro="dbKeyActions"/>
25 69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	369 <change_format>
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	370 <when input="outWig.outWigType" value="wiggle" format="wig"/>
25 69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	371 </change_format>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	372 </data>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	373 </xml>
32 4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	374 <xml name="quantTranscriptomeSAMoutput_param">
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	375 <param argument="--quantTranscriptomeSAMoutput" type="select" label="Alignment filtering for TranscriptomeSAM output">
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	376 <option value="BanSingleEnd_BanIndels_ExtendSoftclip" selected="true">prohibit indels and single-end alignments, extend softclips - compatible with RSEM</option>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	377 <option value="BanSingleEnd">prohibit single-end alignments, allow indels and softclips</option>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	378 <option value="BanSingleEnd_ExtendSoftclip">prohibit single-end alignments, extend softclips, allow indels</option>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	379 </param>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	380 </xml>
25 69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	381 <xml name="quantMode">
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	382 <conditional name="quantmode_output">
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	383 <param argument="--quantMode" type="select" label="Per gene/transcript output" help="STAR can provide analysis results not only with respect to the reference genome, but also with respect to genes and transcripts described by a gene model. Note: This functionality requires either the selection above of a cached index with a gene model, or a gene model provided alongside the index/reference genome in GTF or GFF3 format!">
25 69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	384 <option value="-">No per gene or transcript output</option>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	385 <option value="GeneCounts">Per gene read counts (GeneCounts)</option>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	386 <option value="TranscriptomeSAM">Transcript-based BAM output (TranscriptomeSAM)</option>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	387 <option value="TranscriptomeSAM GeneCounts">Both per gene read counts and transcript-based BAM output (TranscriptomeSAM GeneCounts)</option>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	388 </param>
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	389 <when value="-"/>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	390 <when value="GeneCounts"/>
25 69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	391 <when value="TranscriptomeSAM">
32 4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	392 <expand macro="quantTranscriptomeSAMoutput_param"/>
25 69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	393 </when>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	394 <when value="TranscriptomeSAM GeneCounts">
32 4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	395 <expand macro="quantTranscriptomeSAMoutput_param"/>
25 69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	396 </when>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	397 </conditional>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	398 </xml>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	399 <xml name="quantModeNoGTF">
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	400 <conditional name="quantmode_output">
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	401 <param argument="--quantMode" type="select" label="Per gene/transcript output">
25 69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	402 <option value="-">No per gene or transcript output as no GTF was provided</option>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	403 </param>
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	404 <when value="-"/>
25 69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	405 </conditional>
69780e27bdc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 20 diff changeset	406 </xml>
26 426c1546c6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17 iuc parents: 25 diff changeset	407 <xml name="outSAMmapqUnique">
426c1546c6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17 iuc parents: 25 diff changeset	408 <!-- MAPQ 255 is the default in STAR (coming from tophat behaviour and compatibility for Cufflinks) but it is a problematic value
426c1546c6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17 iuc parents: 25 diff changeset	409 - according to SAM/BAM specs it means "undefined".
426c1546c6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17 iuc parents: 25 diff changeset	410 - Using 255 as the max mapq causes problem with modern downstream tools like mutect2: https://sites.duke.edu/workblog/2021/08/18/star-rnaseq-gatk-mutect2/ and 60 has become an inofficial replacement for 255. -->
30 acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	411 <param argument="--outSAMmapqUnique" type="integer" value="60" min="0" max="255" label="MAPQ value for unique mappers" help="STAR bases the mapping quality scores of alignment records in its BAM output on the number of alternative mappings for the read. If a read maps to multiple locations on the reference genome, the following MAPQ scoring scheme is used: >=5 mappings => MAPQ=0; 3-4 mappings => MAPQ=1; 2 mappings => MAPQ=3. This setting lets you control the MAPQ used for reads mapped to a single location. Set to 255 for compatibility with Cufflink (default in STAR) but keep to 60 for modern downstream tools like mutect2."/>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	412 </xml>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	413 <xml name="wasp">
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	414 <!--
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	415 This is re-implementation of the original WASP algorithm by Bryce van de Geijn, Graham McVicker,
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	416 Yoav Gilad and Jonathan K Pritchard. Please cite the original WASP paper: Nature Methods 12,
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	417 1061–1063 (2015) https://www.nature.com/articles/nmeth.3582. WASP filtering is activated
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	418 with "waspOutputMode SAMtag".
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	419 -->
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	420 <conditional name="wasp_conditional">
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	421 <param argument="--waspOutputMode" type="select" label="Actiavte WASP filtering">
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	422 <help><![CDATA[This is a reimplementation of the original WASP algorithm by Bryce van de Geijn, Graham McVicker,
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	423 Yoav Gilad and Jonathan K Pritchard. https://doi.org/10.1038/nmeth.3582. This option will add the vW tag to the SAM output. vW:i:1 means
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	424 alignment passed WASP filtering, and all other values mean it did not:<br/>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	425 - vW:i:2 = multi-mapping read<br/>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	426 - vW:i:3 = variant base in the read is N (non-ACGT)<br/>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	427 - vW:i:4 = remapped read did not map <br/>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	428 - vW:i:5 = remapped read multi-maps <br/>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	429 - vW:i:6 = remapped read maps to a different locus <br/>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	430 - vW:i:7 = read overlaps too many variants <br/>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	431 ]]>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	432 </help>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	433 <option value="" selected="true">No WASP filtering</option>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	434 <option value="wasp_mode">Activate WASP filtering</option>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	435 </param>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	436 <when value="wasp_mode">
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	437 <param argument="--varVCFfile" type="data" format="vcf" label="VCF file with personal variants" help="Each variant is expected to have a genotype with two alleles. The VCF file needs to have the 10th column with genotype recorded as 0/1, 1/0, 1/1 (or \| instead of /)"/>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	438 </when>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	439 <when value=""/>
acd651be2b9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 iuc parents: 29 diff changeset	440 </conditional>
26 426c1546c6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17 iuc parents: 25 diff changeset	441 </xml>
32 4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	442 <xml name="full_algo_params">
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	443 <section name="seed" title="Seed parameters" expanded="false">
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	444 <param argument="--seedSearchStartLmax" type="integer" min="1" value="50" label="Search start point through the read"/>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	445 <param argument="--seedSearchStartLmaxOverLread" type="float" min="0" value="1.0" label="Search start point through the read, normalized to read length"/>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	446 <param argument="--seedSearchLmax" type="integer" min="0" value="0" label="Maximum length of seeds" help="Default of 0 indicates no maximum length"/>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	447 <param argument="--seedMultimapNmax" type="integer" min="1" value="10000" label="Maximum number of mappings to use a piece in stitching"/>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	448 <param argument="--seedPerReadNmax" type="integer" min="1" value="1000" label="Maximum number of seeds per read"/>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	449 <param argument="--seedPerWindowNmax" type="integer" min="1" value="50" label="Maximum number of seeds per window"/>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	450 <param argument="--seedNoneLociPerWindow" type="integer" min="1" value="10" label="Maximum number of one seed loci per window"/>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	451 </section>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	452 <section name="align" title="Alignment parameters" expanded="false">
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	453 <param argument="--alignIntronMin" type="integer" min="0" value="21" label="Minimum intron size"/>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	454 <param argument="--alignIntronMax" type="integer" min="0" value="0" label="Maximum intron size"/>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	455 <param argument="--alignMatesGapMax" type="integer" min="0" value="0" label="Maximum gap between two mates"/>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	456 <param argument="--alignSJoverhangMin" type="integer" min="1" value="5" label="Minimum overhang for spliced alignments"/>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	457 <section name="alignSJstitchMismatchNmax" title="Maximum number of mismatches for stitching of the splice junctions (-1: no limit)" expanded="true">
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	458 <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax1" type="integer" min="-1" value="0" label="Non-canonical motifs"/>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	459 <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax2" type="integer" min="-1" value="-1" label="GT/AG and CT/AC motif"/>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	460 <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax3" type="integer" min="-1" value="0" label="GC/AG and CT/GC motif"/>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	461 <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax4" type="integer" min="-1" value="0" label="AT/AC and GT/AT motif"/>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	462 </section>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	463 <param argument="--alignSJDBoverhangMin" type="integer" min="1" value="3" label="Minimum overhang for annotated spliced alignments"/>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	464 <param argument="--alignSplicedMateMapLmin" type="integer" min="0" value="0" label="Minimum mapped length for a read mate that is spliced"/>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	465 <param argument="--alignSplicedMateMapLminOverLmate" type="float" min="0" value="0.66" label="Minimum mapped length for a read mate that is spliced, normalized to mate length"/>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	466 <param argument="--alignWindowsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of windows per read"/>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	467 <param argument="--alignTranscriptsPerWindowNmax" type="integer" min="1" value="100" label="Maximum number of transcripts per window"/>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	468 <param argument="--alignTranscriptsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of different alignments per read to consider"/>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	469 <param argument="--alignEndsType" type="select" label="type of read ends alignment">
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	470 <option value="Local">standard local alignment with soft-clipping allowed</option>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	471 <option value="EndToEnd">force end-to-end read alignment, do not soft-clip</option>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	472 <option value="Extend5pOfRead1">fully extend only the 5p of the read1, all other ends: local alignment</option>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	473 <option value="Extend5pOfReads12">fully extend only the 5p of the both read1 and read2, all other ends: local alignment</option>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	474 </param>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	475 <param argument="--peOverlapNbasesMin" type="integer" min="0" value="0"
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	476 label="minimum number of overlap bases to trigger mates merging and realignment" />
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	477 <param argument="--peOverlapMMp" type="float" min="0" max="1" value="0.01"
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	478 label="maximum proportion of mismatched bases in the overlap area" />
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	479 </section>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	480 <section name="chim_settings" title="Chimeric alignment parameters" expanded="false">
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	481 <param argument="--chimSegmentMin" type="integer" min="1" value="12"
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	482 label="Minimum length of chimeric segment"
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	483 help="For small numbers this will cause large number of chimeric alignments. A value of 12 is commonly used." />
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	484 <param argument="--chimScoreMin" type="integer" min="0" value="0"
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	485 label="Minimum total (summed) score of chimeric segments"/>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	486 <param argument="--chimScoreDropMax" type="integer" min="0" value="20"
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	487 label="Maximum difference of chimeric score from read length"/>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	488 <param argument="--chimScoreSeparation" type="integer" min="0" value="10"
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	489 label="Minimum difference between the best chimeric score and the next one"/>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	490 <param argument="--chimScoreJunctionNonGTAG" type="integer" value="-1"
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	491 label="Penalty for a non-GT/AG chimeric junction"/>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	492 <param argument="--chimJunctionOverhangMin" type="integer" min="0" value="20"
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	493 label="Minimum overhang for a chimeric junction"/>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	494 <param argument="--chimSegmentReadGapMax" type="integer" min="0" value="0"
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	495 label="Maximum gap in the read sequence between chimeric segments" />
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	496 <param argument="--chimFilter" type="boolean" truevalue="banGenomicN" falsevalue="None" checked="true"
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	497 label="Discard chimeric alignments with Ns in the genome sequence around the chimeric junction" />
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	498 <param argument="--chimMainSegmentMultNmax" type="integer" min="1" value="10"
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	499 label="Maximum number of multi-alignments for the main chimeric segment."
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	500 help="A value of 1 prohibits multimapping main segments"/>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	501 <param argument="--chimMultimapNmax" type="integer" min="1" value="1"
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	502 label="Maximum number of chimeric multi-alignments"
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	503 help="The default value of 1 only considers unique alignments. If you chose to report chimeric alignments alongside regular ones in the BAM output, this setting is ignored and only uniquely mapping chimeric reads get reported. " />
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	504 <param argument="--chimMultimapScoreRange" type="integer" min="0" value="1"
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	505 label="Score range for multi-mapping chimeras"
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	506 help="The threshold below the best chimeric score that a multimapping chimera must have to be output. This is ignored unless --chimMultimapNmax is above 1" />
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	507 </section>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	508 <expand macro="limits" />
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	509 </xml>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	510 <xml name="chim_params">
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	511 <param argument="--chimOutType" type="select"
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	512 label="Report chimeric alignments?"
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	513 help="Choose if and how chimeric alignments should be reported. STAR-Fusion users should select the 'Junctions' option and use the resulting tabular dataset as input to STAR-Fusion. Everyone else: note that selecting 'WithinBAM' or 'WithinBAM Junctions' disables the --chimMultimapNmax setting in the algorithmic parameters section below (the tool will only consider uniquely mapped reads in the search for chimeric alignments). If you disable the reporting of chimeric alignments here, then all chimeric alignment settings in the algorithmic parameters section below will be ignored.">
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	514 <option value="">Don't report chimeric alignments</option>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	515 <option value="Junctions">As separate tabular "Junctions" output (Junctions)</option>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	516 <option value="WithinBAM">Within the BAM output (together with regular alignments; WithinBAM)</option>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	517 <option value="WithinBAM HardClip">Within the BAM output (together with regular alignments; WithinBAM HardClip) hard-clipping in the CIGAR for supplemental chimeric alignments</option>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	518 <option value="WithinBAM SoftClip">Within the BAM output (together with regular alignments; WithinBAM SoftClip) soft-clipping in the CIGAR for supplemental chimeric alignments</option>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	519 </param>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	520 </xml>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	521 <token name="@ALGO_FULL@"><![CDATA[
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	522 ## Extended parameter options
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	523
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	524 ## Seed parameter options
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	525 --seedSearchStartLmax ${algo.params.seed.seedSearchStartLmax}
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	526 --seedSearchStartLmaxOverLread ${algo.params.seed.seedSearchStartLmaxOverLread}
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	527 --seedSearchLmax ${algo.params.seed.seedSearchLmax}
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	528 --seedMultimapNmax ${algo.params.seed.seedMultimapNmax}
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	529 --seedPerReadNmax ${algo.params.seed.seedPerReadNmax}
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	530 --seedPerWindowNmax ${algo.params.seed.seedPerWindowNmax}
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	531 --seedNoneLociPerWindow ${algo.params.seed.seedNoneLociPerWindow}
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	532
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	533 ## Alignment parameter options
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	534 --alignIntronMin ${algo.params.align.alignIntronMin}
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	535 --alignIntronMax ${algo.params.align.alignIntronMax}
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	536 --alignMatesGapMax ${algo.params.align.alignMatesGapMax}
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	537 --alignSJoverhangMin ${algo.params.align.alignSJoverhangMin}
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	538 --alignSJstitchMismatchNmax ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax1} ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax2} ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax3} ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax4}
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	539 --alignSJDBoverhangMin ${algo.params.align.alignSJDBoverhangMin}
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	540 --alignSplicedMateMapLmin ${algo.params.align.alignSplicedMateMapLmin}
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	541 --alignSplicedMateMapLminOverLmate ${algo.params.align.alignSplicedMateMapLminOverLmate}
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	542 --alignWindowsPerReadNmax ${algo.params.align.alignWindowsPerReadNmax}
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	543 --alignTranscriptsPerWindowNmax ${algo.params.align.alignTranscriptsPerWindowNmax}
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	544 --alignTranscriptsPerReadNmax ${algo.params.align.alignTranscriptsPerReadNmax}
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	545 --alignEndsType ${algo.params.align.alignEndsType}
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	546 --peOverlapNbasesMin ${algo.params.align.peOverlapNbasesMin}
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	547 --peOverlapMMp ${algo.params.align.peOverlapMMp}
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	548 ## Chimeric alignment parameter options
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	549 #if str($chimOutType):
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	550 --chimSegmentMin ${algo.params.chim_settings.chimSegmentMin}
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	551 --chimScoreMin ${algo.params.chim_settings.chimScoreMin}
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	552 --chimScoreDropMax $algo.params.chim_settings.chimScoreDropMax
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	553 --chimScoreSeparation $algo.params.chim_settings.chimScoreSeparation
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	554 --chimScoreJunctionNonGTAG $algo.params.chim_settings.chimScoreJunctionNonGTAG
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	555 --chimSegmentReadGapMax $algo.params.chim_settings.chimSegmentReadGapMax
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	556 --chimFilter $algo.params.chim_settings.chimFilter
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	557 --chimJunctionOverhangMin $algo.params.chim_settings.chimJunctionOverhangMin
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	558 --chimMainSegmentMultNmax $algo.params.chim_settings.chimMainSegmentMultNmax
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	559 #if str($chimOutType) == 'Junctions':
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	560 --chimMultimapNmax $algo.params.chim_settings.chimMultimapNmax
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	561 #else:
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	562 --chimMultimapNmax 0
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	563 #end if
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	564 --chimMultimapScoreRange $algo.params.chim_settings.chimMultimapScoreRange
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	565 #end if
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	566
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	567 ## Limits
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	568 @LIMITS@
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	569 ]]></token>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	570 <token name="@ALGO_DEFAULT@"><![CDATA[
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	571 ## Go with STAR's default algorithmic settings,
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	572 ## but we need to provide a reasonable default
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	573 ## (taken from STAR-Fusion)
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	574 ## for --chimSegmentMin in case the user enabled chimeric
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	575 ## alignments (the STAR default is 0, which disables chimeric
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	576 ## alignments). For consistency, also set
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	577 ## --chimMultimapNmax to 1 when chimeric alignments are reported
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	578 ## in Junctions format only.
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	579 #if str($chimOutType):
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	580 --chimSegmentMin 12
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	581 #if str($chimOutType) == 'Junctions':
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	582 --chimMultimapNmax 1
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	583 #end if
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	584 #end if
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	585 ]]></token>
4746de55986e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256 iuc parents: 31 diff changeset	586
4 13dba3e91459 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: diff changeset	587 </macros>

Mercurial > repos > iuc > rgrnastar

annotate macros.xml @ 32:4746de55986e draft default tip