rgrnastar: macros.xml annotate

annotate macros.xml @ 23:a2b0feda6933 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266

author	iuc
date	Fri, 17 Feb 2023 20:03:27 +0000
parents	c772497b2c32
children	4df95e2d7f61

rev	line source
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: diff changeset	1 <macros>
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	2 <!-- REMEMBER to bump the version of @IDX_VERSION_SUFFIX@
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	3 whenever you make changes to the @TOOL_VERSION@ token!
14 b9e04854e2bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e" iuc parents: 13 diff changeset	4 The data manager uses a symlink to this macro file to keep the STAR and
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	5 the index versions in sync, but you should manually update @IDX_VERSION_SUFFIX@ -->
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	6 <!-- STAR version to be used -->
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	7 <token name="@TOOL_VERSION@">2.7.10b</token>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	8 <token name="@VERSION_SUFFIX@">0</token>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	9 <token name="@PROFILE@">21.01</token>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	10 <!-- STAR index version compatible with this version of STAR
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	11 This is the STAR version that introduced the index structure expected
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	12 by the current version.
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	13 It can be found for any specific version of STAR with:
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	14 STAR -h \| grep versionGenome
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	15 or by looking for the versionGenome parameter in source/parametersDefault
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	16 of STAR's source code -->
15 5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 14 diff changeset	17 <token name="@IDX_VERSION@">2.7.4a</token>
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	18 <token name="@IDX_VERSION_SUFFIX@">1</token>
15 5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 14 diff changeset	19 <token name="@IDX_DATA_TABLE@">rnastar_index2x_versioned</token>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	20
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: diff changeset	21 <xml name="requirements">
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: diff changeset	22 <requirements>
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	23 <requirement type="package" version="@TOOL_VERSION@">star</requirement>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	24 <requirement type="package" version="1.16.1">samtools</requirement>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	25 <requirement type="package" version="1.12">gzip</requirement>
14 b9e04854e2bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e" iuc parents: 13 diff changeset	26 <yield />
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: diff changeset	27 </requirements>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: diff changeset	28 </xml>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	29
16 e132e7d02a3e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9c34fd08b619a09028707a52c868d9be1ca02a6b" iuc parents: 15 diff changeset	30 <xml name="edam">
e132e7d02a3e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9c34fd08b619a09028707a52c868d9be1ca02a6b" iuc parents: 15 diff changeset	31 <edam_topics>
e132e7d02a3e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9c34fd08b619a09028707a52c868d9be1ca02a6b" iuc parents: 15 diff changeset	32 <edam_topic>topic_3170</edam_topic>
e132e7d02a3e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9c34fd08b619a09028707a52c868d9be1ca02a6b" iuc parents: 15 diff changeset	33 <edam_topic>topic_3308</edam_topic>
e132e7d02a3e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9c34fd08b619a09028707a52c868d9be1ca02a6b" iuc parents: 15 diff changeset	34 </edam_topics>
e132e7d02a3e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9c34fd08b619a09028707a52c868d9be1ca02a6b" iuc parents: 15 diff changeset	35 <edam_operations>
e132e7d02a3e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9c34fd08b619a09028707a52c868d9be1ca02a6b" iuc parents: 15 diff changeset	36 <edam_operation>operation_0292</edam_operation>
e132e7d02a3e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9c34fd08b619a09028707a52c868d9be1ca02a6b" iuc parents: 15 diff changeset	37 </edam_operations>
e132e7d02a3e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9c34fd08b619a09028707a52c868d9be1ca02a6b" iuc parents: 15 diff changeset	38 </xml>
17 7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	39
11 41929aa1e7f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2911002ccd79fe062f6346ee5699ea262f92f04f" iuc parents: 10 diff changeset	40 <xml name="index_selection" token_with_gene_model="0">
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	41 <param argument="--genomeDir" type="select"
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	42 label="Select reference genome"
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	43 help="If your genome of interest is not listed, contact the Galaxy team">
15 5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 14 diff changeset	44 <options from_data_table="@IDX_DATA_TABLE@">
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	45 <filter type="static_value" column="4" value="@WITH_GENE_MODEL@" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	46 <filter type="static_value" column="5" value="@IDX_VERSION@" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	47 <filter type="sort_by" column="2" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	48 <validator type="no_options" message="No indexes are available for the selected input dataset" />
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	49 </options>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	50 </param>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	51 </xml>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	52
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: diff changeset	53 <token name="@FASTQ_GZ_OPTION@">
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: diff changeset	54 --readFilesCommand zcat
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: diff changeset	55 </token>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: diff changeset	56 <xml name="citations">
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: diff changeset	57 <citations>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: diff changeset	58 <citation type="doi">10.1093/bioinformatics/bts635</citation>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: diff changeset	59 </citations>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: diff changeset	60 </xml>
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	61 <xml name="SJDBOPTIONS">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	62 <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"/>
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: diff changeset	63 <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"/>
318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: diff changeset	64 </xml>
8 d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	65 <xml name="dbKeyActions">
d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	66 <actions>
d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	67 <conditional name="refGenomeSource.geneSource">
d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	68 <when value="indexed">
d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	69 <action type="metadata" name="dbkey">
15 5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 14 diff changeset	70 <option type="from_data_table" name="@IDX_DATA_TABLE@" column="1" offset="0">
8 d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	71 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	72 <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	73 </option>
d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	74 </action>
d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	75 </when>
d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	76 <when value="history">
d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	77 <action type="metadata" name="dbkey">
d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	78 <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	79 </action>
d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	80 </when>
d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	81 </conditional>
d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	82 </actions>
d5659efd66aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167 iuc parents: 7 diff changeset	83 </xml>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	84 <token name="@TEMPINDEX@"><![CDATA[
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	85 ## Create temporary index for custom reference
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	86 #if str($refGenomeSource.geneSource) == 'history':
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	87 #if $refGenomeSource.genomeFastaFiles.ext == "fasta"
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	88 ln -s '$refGenomeSource.genomeFastaFiles' refgenome.fa &&
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	89 #else
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	90 gunzip -c '$refGenomeSource.genomeFastaFiles' > refgenome.fa &&
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	91 #end if
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	92 mkdir -p tempstargenomedir &&
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	93 STAR
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	94 --runMode genomeGenerate
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	95 --genomeDir 'tempstargenomedir'
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	96 --genomeFastaFiles refgenome.fa
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	97 ## Handle difference between indices with/without annotations
15 5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 14 diff changeset	98 #if 'GTFconditional' in $refGenomeSource:
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 14 diff changeset	99 ## GTFconditional exists only in STAR, but not STARsolo
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 14 diff changeset	100 #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf':
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 14 diff changeset	101 --sjdbOverhang '${refGenomeSource.GTFconditional.sjdbOverhang}'
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 14 diff changeset	102 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 14 diff changeset	103 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 14 diff changeset	104 --sjdbGTFtagExonParentTranscript Parent
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 14 diff changeset	105 #end if
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 14 diff changeset	106 #end if
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 14 diff changeset	107 #else:
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 14 diff changeset	108 ## ref genome selection is less complex for STARsolo cause
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 14 diff changeset	109 ## with-gtf is mandatory there
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 14 diff changeset	110 --sjdbOverhang '${refGenomeSource.sjdbOverhang}'
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 14 diff changeset	111 --sjdbGTFfile '${refGenomeSource.sjdbGTFfile}'
5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 14 diff changeset	112 #if str($refGenomeSource.sjdbGTFfile.ext) == 'gff3':
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	113 --sjdbGTFtagExonParentTranscript Parent
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	114 #end if
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	115 #end if
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	116 #if str($refGenomeSource.genomeSAindexNbases):
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	117 --genomeSAindexNbases ${refGenomeSource.genomeSAindexNbases}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	118 #end if
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	119 --runThreadN \${GALAXY_SLOTS:-4}
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	120 ## in bytes
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	121 --limitGenomeGenerateRAM \$((\${GALAXY_MEMORY_MB:-31000} * 1000000))
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	122 &&
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	123 #end if
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	124 ]]></token>
12 39bde80cd248 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba" iuc parents: 11 diff changeset	125 <token name="@REFGENOMEHANDLING@" ><![CDATA[
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	126 --runThreadN \${GALAXY_SLOTS:-4}
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	127 --genomeLoad NoSharedMemory
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	128 --genomeDir
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	129 #if str($refGenomeSource.geneSource) == 'history':
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	130 tempstargenomedir
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	131 #else:
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	132 '${refGenomeSource.GTFconditional.genomeDir.fields.path}'
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	133 ## Handle difference between indices with/without annotations
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	134 #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf-with-gtf':
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	135 --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	136 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	137 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	138 --sjdbGTFtagExonParentTranscript Parent
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	139 #end if
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	140 #end if
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	141 #end if
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	142 ]]></token>
17 7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	143 <token name="@READSHANDLING@" ><![CDATA[
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	144 ## Check that the input pairs are of the same type
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	145 ## otherwise STARsolo will run for a long time and then error out.
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	146 ## We consume either repeats of two inputs R1 + R2
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	147 ## or a collection of paired reads.
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	148 #if str($sc.input_types.use) == "repeat":
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	149 #set $reads1 = []
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	150 #set $reads2 = []
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	151 #for $r1, $r2 in zip($sc.input_types.input1, $sc.input_types.input2):
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	152 #assert $r1.datatype == $r2.datatype
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	153 #silent $reads1.append(str($r1))
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	154 #silent $reads2.append(str($r2))
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	155 #end for
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	156 #set $reads1 = ','.join($reads1)
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	157 #set $reads2 = ','.join($reads2)
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	158 #elif str($sc.input_types.use) == "list_paired":
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	159 #set $r1 = $sc.input_types.input_collection.forward
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	160 #set $r2 = $sc.input_types.input_collection.reverse
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	161 #set $reads1 = $r1
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	162 #set $reads2 = $r2
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	163 #end if
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	164 ## cDNA sequence(s) [R2] always go first, then barcode(s) [R1]
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	165 ## see: Section 3.2 of STAR manual for multiple inputs, and Section 13 for STARsolo inputs
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	166 --readFilesIn $reads2 $reads1
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	167 --soloCBmatchWLtype $sc.soloCBmatchWLtype
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	168 #if $r1.is_of_type('fastq.gz', 'fastqsanger.gz'):
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	169 @FASTQ_GZ_OPTION@
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	170 #end if
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	171 ]]></token>
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	172 <token name="@LIMITS@" ><![CDATA[
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	173 --limitOutSJoneRead $getVar('algo.params.junction_limits.limitOutSJoneRead', $getVar('solo.junction_limits.limitOutSJoneRead', 1000))
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	174 --limitOutSJcollapsed $getVar('algo.params.junction_limits.limitOutSJcollapsed', $getVar('solo.junction_limits.limitOutSJcollapsed', 1000000))
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	175 --limitSjdbInsertNsj $getVar('algo.params.junction_limits.limitSjdbInsertNsj', $getVar('solo.junction_limits.limitSjdbInsertNsj', 1000000))
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	176 ]]></token>
15 5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 14 diff changeset	177 <xml name="ref_selection">
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	178 <param argument="--genomeFastaFiles" type="data" format="fasta,fasta.gz" label="Select a reference genome" />
18 c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 17 diff changeset	179 <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)"/>
15 5ec75f5dae3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9" iuc parents: 14 diff changeset	180 </xml>
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	181 <xml name="stdio" >
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	182 <stdio>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	183 <regex match="FATAL error" source="both" level="fatal"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	184 <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	185 <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	186 <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/>
12 39bde80cd248 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba" iuc parents: 11 diff changeset	187 <yield />
10 d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	188 </stdio>
d82339e37e8e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97" iuc parents: 8 diff changeset	189 </xml>
17 7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	190 <xml name="input_selection">
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	191 <conditional name="input_types" >
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	192 <param name="use" type="select" label="Input Type" >
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	193 <option value="repeat" >Separate barcode and cDNA reads</option>
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	194 <option value="list_paired" >Paired collection of barcode and cDNA reads</option>
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	195 </param>
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	196 <when value="repeat">
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	197 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" multiple="true"
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	198 label="RNA-Seq FASTQ/FASTA file, Barcode reads" />
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	199 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input2" type="data" multiple="true"
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	200 label="RNA-Seq FASTQ/FASTA file, cDNA reads"/>
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	201 </when>
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	202 <when value="list_paired">
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	203 <param name="input_collection" collection_type="paired" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="Collection of Pairs" />
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	204 </when>
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	205 </conditional>
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	206 </xml>
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	207 <xml name="input_selection_smart_seq">
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	208 <conditional name="input_types_smart_seq" >
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	209 <param name="use" type="select" label="Input Type" >
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	210 <option value="list_single_end" >Single-end FASTQ collection</option>
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	211 <option value="list_paired_end" >Paired FASTQ collection</option>
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	212 </param>
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	213 <when value="list_single_end">
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	214 <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" />
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	215 </when>
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	216 <when value="list_paired_end">
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	217 <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" />
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	218 </when>
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	219 </conditional>
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	220 </xml>
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	221 <xml name="umidedup_options">
18 c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 17 diff changeset	222 <option value="1MM_All" selected="true">Collapse all UMIs with 1 mismatch distance to each other</option>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 17 diff changeset	223 <option value="1MM_Directional_UMItools" >Directional method from the UMI-tool</option>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 17 diff changeset	224 <option value="1MM_Directional" >Directional with stringent UMI deduplication</option>
17 7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	225 </xml>
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	226 <xml name="anchor_types">
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	227 <option value="0">Read start</option>
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	228 <option value="1">Read end</option>
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	229 <option value="2">Adapter start</option>
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	230 <option value="3">Adapter end</option>
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	231 </xml>
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	232 <xml name="cb_match_wl_common">
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	233 <option value="Exact" >Exact</option>
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	234 <option value="1MM" >Single match</option>
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	235 </xml>
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	236 <xml name="cb_match_wl_cellranger">
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	237 <option value="1MM_multi" selected="true" >Multiple matches (CellRanger 2)</option>
7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	238 <option value="1MM_multi_pseudocounts" >Multiple matches (CellRanger 3)</option>
18 c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 17 diff changeset	239 <option value="1MM_multi_Nbase_pseudocounts" >Multimatching to WL is allowed for CBs with N-bases (CellRanger 3)</option>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 17 diff changeset	240 </xml>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 17 diff changeset	241 <xml name="solo_adapter_params">
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 17 diff changeset	242 <param argument="--soloAdapterSequence" type="text" value="-" label="Adapter sequence to anchor barcodes." >
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 17 diff changeset	243 <sanitizer>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 17 diff changeset	244 <valid initial="string.digits">
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 17 diff changeset	245 <add value="-"/>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 17 diff changeset	246 <add value="A"/>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 17 diff changeset	247 <add value="T"/>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 17 diff changeset	248 <add value="C"/>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 17 diff changeset	249 <add value="G"/>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 17 diff changeset	250 <add value="N"/>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 17 diff changeset	251 </valid>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 17 diff changeset	252 </sanitizer>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 17 diff changeset	253 </param>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 17 diff changeset	254 <param argument="--soloAdapterMismatchesNmax" type="integer" min="1" value="1" label="Maximum number of mismatches allowed in adapter sequence" />
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 17 diff changeset	255 <param argument="--clipAdapterType" type="select" >
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 17 diff changeset	256 <option value="Hamming" selected="true" >Adapter clipping based on Hamming distance</option>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 17 diff changeset	257 <option value="CellRanger4" >5p and 3p adapter clipping similar to CellRanger4</option>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 17 diff changeset	258 <option value="None" >No adapter clipping</option>
c772497b2c32 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9" iuc parents: 17 diff changeset	259 </param>
17 7ed2edc1337f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531" iuc parents: 16 diff changeset	260 </xml>
23 a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	261 <xml name="common_SAM_attributes">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	262 <option value="NH" selected="true">NH (number of reported alignments/hits for the read)</option>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	263 <option value="HI" selected="true">HI (query hit index)</option>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	264 <option value="AS" selected="true">AS (local alignment score)</option>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	265 <option value="nM" selected="true">nM (number of mismatches per (paired) alignment)</option>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	266 <option value="NM">NM (edit distance of the aligned read to the reference)</option>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	267 <option value="MD">MD (string for mismatching positions)</option>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	268 <option value="jM">jM (intron motifs for all junctions)</option>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	269 <option value="jI">jI (1-based start and end of introns for all junctions)</option>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	270 </xml>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	271 <xml name="limits">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	272 <section name="junction_limits" title="Junction Limits" expanded="false">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	273 <param argument="--limitOutSJoneRead" type="integer" min="1" value="1000" label="Maximum number of junctions for one read (including all multimappers)" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	274 <param argument="--limitOutSJcollapsed" type="integer" min="1" value="1000000" label="Maximum number of collapsed junctions" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	275 <param argument="--limitSjdbInsertNsj" type="integer" min="0" value="1000000" label="Maximum number of inserts to be inserted into the genome on the fly." />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	276 </section>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	277 </xml>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	278 <xml name="outCountActions">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	279 <actions>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	280 <action name="column_names" type="metadata" default="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	281 </actions>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	282 </xml>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	283 <xml name="outWig">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	284 <conditional name="outWig">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	285 <param name="outWigType" type="select" label="Compute coverage">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	286 <option value="None">No coverage</option>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	287 <option value="bedGraph">Yes in bedgraph format</option>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	288 <option value="wiggle">Yes in wiggle format</option>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	289 </param>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	290 <when value="None">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	291 <!-- This is necessary for the filtering of output -->
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	292 <param name="outWigStrand" type="hidden" value="false" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	293 </when>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	294 <when value="bedGraph">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	295 <expand macro="outWigParams"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	296 </when>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	297 <when value="wiggle">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	298 <expand macro="outWigParams"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	299 </when>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	300 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	301 </xml>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	302 <xml name="outWigParams">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	303 <param name="outWigTypeSecondWord" type="select" label="Input for coverage">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	304 <option value="">Default (everything that mapped)</option>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	305 <option value="read_5p">signal from only 5’ of the 1st read</option>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	306 <option value="read2">signal from only 2nd read</option>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	307 </param>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	308 <param argument="--outWigStrand" type="boolean" truevalue="Stranded" falsevalue="Unstranded" checked="true" label="collapse strands (unstranded coverage)" help="By default, the strands are separated."/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	309 <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"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	310 <param argument="--outWigNorm" type="boolean" truevalue="RPM" falsevalue="None" checked="true" label="Normalize coverage to million of mapped reads (RPM)"/>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	311 </xml>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	312 <token name="@OUTWIG@"><![CDATA[
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	313 #if str($outWig.outWigType) != 'None':
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	314 --outWigType '$outWig.outWigType' '$outWig.outWigTypeSecondWord'
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	315 --outWigStrand '$outWig.outWigStrand'
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	316 --outWigReferencesPrefix '$outWig.outWigReferencesPrefix'
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	317 --outWigNorm '$outWig.outWigNorm'
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	318 #end if
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	319 ]]></token>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	320 <token name="@OUTWIGOUTPUTS@"><![CDATA[
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	321 #if str($outWig.outWigType) == "bedGraph":
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	322 && mv Signal.Unique.str1.out.bg Signal.Unique.str1.out
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	323 && mv Signal.UniqueMultiple.str1.out.bg Signal.UniqueMultiple.str1.out
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	324 #if str($outWig.outWigStrand) == "Stranded":
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	325 && mv Signal.Unique.str2.out.bg Signal.Unique.str2.out
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	326 && mv Signal.UniqueMultiple.str2.out.bg Signal.UniqueMultiple.str2.out
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	327 #end if
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	328 #elif str($outWig.outWigType) == "wiggle":
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	329 && mv Signal.Unique.str1.out.wig Signal.Unique.str1.out
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	330 && mv Signal.UniqueMultiple.str1.out.wig Signal.UniqueMultiple.str1.out
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	331 #if str($outWig.outWigStrand) == "Stranded":
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	332 && mv Signal.Unique.str2.out.wig Signal.Unique.str2.out
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	333 && mv Signal.UniqueMultiple.str2.out.wig Signal.UniqueMultiple.str2.out
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	334 #end if
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	335 #end if
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	336 ]]></token>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	337 <xml name="outWigOutputs">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	338 <data format="bedgraph" name="signal_unique_str1" label="${tool.name} on ${on_string}: Coverage Uniquely mapped strand 1" from_work_dir="Signal.Unique.str1.out">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	339 <filter>outWig['outWigType'] != "None"</filter>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	340 <expand macro="dbKeyActions" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	341 <change_format>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	342 <when input="outWig.outWigType" value="wiggle" format="wig" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	343 </change_format>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	344 </data>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	345 <data format="bedgraph" name="signal_uniquemultiple_str1" label="${tool.name} on ${on_string}: Coverage Uniquely + Multiple mapped strand 1" from_work_dir="Signal.UniqueMultiple.str1.out">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	346 <filter>outWig['outWigType'] != "None"</filter>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	347 <expand macro="dbKeyActions" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	348 <change_format>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	349 <when input="outWig.outWigType" value="wiggle" format="wig" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	350 </change_format>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	351 </data>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	352 <data format="bedgraph" name="signal_unique_str2" label="${tool.name} on ${on_string}: Coverage Uniquely mapped strand 2" from_work_dir="Signal.Unique.str2.out">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	353 <filter>outWig['outWigType'] != "None" and outWig['outWigStrand']</filter>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	354 <expand macro="dbKeyActions" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	355 <change_format>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	356 <when input="outWig.outWigType" value="wiggle" format="wig" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	357 </change_format>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	358 </data>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	359 <data format="bedgraph" name="signal_uniquemultiple_str2" label="${tool.name} on ${on_string}: Coverage Uniquely + Multiple mapped strand 2" from_work_dir="Signal.UniqueMultiple.str2.out">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	360 <filter>outWig['outWigType'] != "None" and outWig['outWigStrand']</filter>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	361 <expand macro="dbKeyActions" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	362 <change_format>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	363 <when input="outWig.outWigType" value="wiggle" format="wig" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	364 </change_format>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	365 </data>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	366 </xml>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	367 <xml name="quantMode">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	368 <conditional name="quantmode_output">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	369 <param argument="--quantMode" type="select"
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	370 label="Per gene/transcript output"
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	371 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!">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	372 <option value="-">No per gene or transcript output</option>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	373 <option value="GeneCounts">Per gene read counts (GeneCounts)</option>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	374 <option value="TranscriptomeSAM">Transcript-based BAM output (TranscriptomeSAM)</option>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	375 <option value="TranscriptomeSAM GeneCounts">Both per gene read counts and transcript-based BAM output (TranscriptomeSAM GeneCounts)</option>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	376 </param>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	377 <when value="-" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	378 <when value="GeneCounts" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	379 <when value="TranscriptomeSAM">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	380 <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend"
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	381 label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?"
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	382 help="You will need to exclude alignments with indels and soft-clipped bases from the transcriptome BAM output for compatibility with certain transcript quantification tools, most notably RSEM. If you are using a tool, like eXpress, that can deal with indels and soft-clipped bases, you can achieve better results by leaving this option disabled." />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	383 </when>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	384 <when value="TranscriptomeSAM GeneCounts">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	385 <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend"
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	386 label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?"
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	387 help="You will need to exclude alignments with indels and soft-clipped bases from the transcriptome BAM output for compatibility with certain transcript quantification tools, most notably RSEM. If you are using a tool, like eXpress, that can deal with indels and soft-clipped bases, you can achieve better results by leaving this option disabled." />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	388 </when>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	389 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	390 </xml>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	391 <xml name="quantModeNoGTF">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	392 <conditional name="quantmode_output">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	393 <param argument="--quantMode" type="select"
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	394 label="Per gene/transcript output">
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	395 <option value="-">No per gene or transcript output as no GTF was provided</option>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	396 </param>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	397 <when value="-" />
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	398 </conditional>
a2b0feda6933 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 iuc parents: 18 diff changeset	399 </xml>
3 318b2a9d54dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1 iuc parents: diff changeset	400 </macros>

Mercurial > repos > iuc > rgrnastar

annotate macros.xml @ 23:a2b0feda6933 draft