Mercurial > repos > iuc > rgrnastar
annotate rg_rnaStar.xml @ 24:4df95e2d7f61 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
author | iuc |
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date | Wed, 22 Feb 2023 18:00:57 +0000 |
parents | a2b0feda6933 |
children | 79de45b5069b |
rev | line source |
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23
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
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1 <tool id="rna_star" name="RNA STAR" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> |
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b2326241bb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
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2 <description>Gapped-read mapper for RNA-seq data</description> |
22
980d2a2e1180
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
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3 <macros> |
980d2a2e1180
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
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4 <import>macros.xml</import> |
980d2a2e1180
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
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5 </macros> |
980d2a2e1180
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
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6 <expand macro="edam"/> |
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e132e7d02a3e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9c34fd08b619a09028707a52c868d9be1ca02a6b"
iuc
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7 <xrefs> |
e132e7d02a3e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9c34fd08b619a09028707a52c868d9be1ca02a6b"
iuc
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8 <xref type="bio.tools">star</xref> |
e132e7d02a3e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9c34fd08b619a09028707a52c868d9be1ca02a6b"
iuc
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9 </xrefs> |
3
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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10 <expand macro="requirements"/> |
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d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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11 <expand macro="stdio" /> |
0
b2326241bb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
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12 |
3
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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13 <!-- |
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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14 important quote (https://groups.google.com/forum/#!topic/rna-star/q4zGzlPgwXY): |
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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15 Hi Gary, |
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
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16 |
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
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17 if you generate the genome with GTF file, and do not specify the value for - -sjdbOverhang, it will be set to the default 100. |
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
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18 If you want to be able to set arbitrary value of - -sjdbOverhang on the fly, you have to generate the genome without annotations (GTF) - then you supply both the - -sjdbOverhang and GTF file at the mapping step. |
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
2
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19 |
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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20 Cheers |
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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21 Alex |
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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22 --> |
1
bc685d13b637
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 97a064489364118d108b0dd2cfb4d9bc53080837
iuc
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23 <command><![CDATA[ |
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d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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24 @TEMPINDEX@ |
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318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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25 STAR |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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26 @REFGENOMEHANDLING@ |
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318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
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27 |
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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28 --readFilesIn |
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d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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29 #if str($singlePaired.sPaired) == 'paired_collection': |
3
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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30 '$singlePaired.input.forward' '$singlePaired.input.reverse' |
2
ace9f5a2b40f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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31 |
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d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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32 #if $singlePaired.input.forward.is_of_type('fastq.gz', 'fastqsanger.gz'): |
3
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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33 @FASTQ_GZ_OPTION@ |
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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34 #end if |
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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35 #else |
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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36 '$singlePaired.input1' |
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d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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37 #if str($singlePaired.sPaired) == 'paired': |
3
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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38 '$singlePaired.input2' |
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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39 #end if |
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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40 |
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d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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41 #if $singlePaired.input1.is_of_type('fastq.gz', 'fastqsanger.gz'): |
3
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
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42 @FASTQ_GZ_OPTION@ |
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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43 #end if |
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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44 #end if |
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
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45 |
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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46 --outSAMtype BAM SortedByCoordinate |
2
ace9f5a2b40f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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47 |
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d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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48 ## Two pass mode |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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49 --twopassMode ${twopass.twopassMode} ${twopass.twopass_read_subset} |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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50 #for $sj_input in $twopass.sj_precalculated: |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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51 '$sj_input' |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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52 #end for |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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53 #if str($twopass.twopassMode) != 'None': |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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54 #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf': |
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91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
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55 ## need to check first if its a cached index or from history |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
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56 ## if it's cached then the sjdbGTFfile and sjdbOverhang params are not provided |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
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57 #if str($refGenomeSource.geneSource) == 'history': |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
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58 #if not $refGenomeSource.GTFconditional.sjdbGTFfile: |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
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59 ## case of cached index without built-in gene model, |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
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60 ## when user does not supply the optional gtf, but |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
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61 ## specifies the splice junction overhang |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
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62 --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
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63 #end if |
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318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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64 #end if |
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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65 #end if |
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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66 #end if |
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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67 |
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a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
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68 --quantMode ${refGenomeSource.GTFconditional.quantmode_output.quantMode} |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
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69 #if 'TranscriptomeSAM' in str($refGenomeSource.GTFconditional.quantmode_output.quantMode): |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
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70 --quantTranscriptomeBan ${refGenomeSource.GTFconditional.quantmode_output.quantTranscriptomeBan} |
2
ace9f5a2b40f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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71 #end if |
0
b2326241bb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
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72 |
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d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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73 ## Output format parameters |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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74 |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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75 ## Read tags |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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76 #set read_tags = str($oformat.outSAMattributes).split(',') |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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77 #if 'XS' in str($oformat.outSAMattributes): |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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78 ## STAR writes XS tag when --outSAMstrandField intronMotif is used |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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79 $read_tags.remove('XS') |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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80 --outSAMstrandField intronMotif |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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81 #end if |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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82 #if 'HI' in str($oformat.outSAMattributes): |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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83 --outSAMattrIHstart ${oformat.HI_offset} |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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84 #end if |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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85 #set $tag_names = ' '.join($read_tags) |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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86 --outSAMattributes $tag_names |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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87 |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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88 ## Read FLAG |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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89 --outSAMprimaryFlag ${oformat.outSAMprimaryFlag} |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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changeset
|
90 |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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91 ## Read MAPQ |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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92 --outSAMmapqUnique ${oformat.outSAMmapqUnique} |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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93 |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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94 ## Output filter parameters |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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95 |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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96 ## Basic Filters |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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97 #if str($filter.basic_filters) != 'None': |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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98 #set $filter_options = str($filter.basic_filters).split(',') |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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99 #else: |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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100 #set filter_options = [] |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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101 #end if |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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102 #if 'exclude_unmapped' in $filter_options: |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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103 $filter_options.remove('exclude_unmapped') |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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104 --outSAMunmapped None |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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105 #else: |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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106 --outSAMunmapped Within |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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107 #end if |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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108 #if '--outFilterIntronMotifs RemoveNoncanonical' in $filter_options: |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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109 ## RemoveNoncanonical excludes a superset of the reads excluded |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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110 ## with RemoveNoncanonicalUnannotated |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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111 #if '--outFilterIntronMotifs RemoveNoncanonicalUnannotated' in $filter_options: |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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112 $filter_options.remove('--outFilterIntronMotifs RemoveNoncanonicalUnannotated') |
7
a70a7eebb435
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 998444037eb7fc93c5dc1441f9c2aecca4b03a7c
iuc
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113 #end if |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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114 #end if |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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115 #echo ' '.join($filter_options) |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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116 |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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117 ## Other Filters |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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118 #if str( $filter.output_params2.output_select2 ) == 'yes': |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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119 --outFilterType $filter.output_params2.outFilterType |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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120 --outFilterMultimapScoreRange $filter.output_params2.outFilterMultimapScoreRange |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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121 --outFilterMultimapNmax $filter.output_params2.outFilterMultimapNmax |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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122 --outFilterMismatchNmax $filter.output_params2.outFilterMismatchNmax |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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123 --outFilterMismatchNoverLmax $filter.output_params2.outFilterMismatchNoverLmax |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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124 --outFilterMismatchNoverReadLmax $filter.output_params2.outFilterMismatchNoverReadLmax |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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125 --outFilterScoreMin $filter.output_params2.outFilterScoreMin |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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126 --outFilterScoreMinOverLread $filter.output_params2.outFilterScoreMinOverLread |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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127 --outFilterMatchNmin $filter.output_params2.outFilterMatchNmin |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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128 --outFilterMatchNminOverLread $filter.output_params2.outFilterMatchNminOverLread |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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129 --outSAMmultNmax $filter.output_params2.outSAMmultNmax |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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130 --outSAMtlen $filter.output_params2.outSAMtlen |
2
ace9f5a2b40f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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131 #end if |
ace9f5a2b40f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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132 |
3
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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133 ## Other parameters |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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134 #if str( $algo.params.settingsType ) == 'star_fusion': |
3
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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135 ## Preset parameters for STAR-Fusion |
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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136 --chimSegmentMin 12 |
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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137 --chimJunctionOverhangMin 12 |
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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138 --alignSJDBoverhangMin 10 |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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139 --alignMatesGapMax 100000 |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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140 --alignIntronMax 100000 |
7
a70a7eebb435
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 998444037eb7fc93c5dc1441f9c2aecca4b03a7c
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141 --chimSegmentReadGapMax 3 |
a70a7eebb435
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 998444037eb7fc93c5dc1441f9c2aecca4b03a7c
iuc
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142 --alignSJstitchMismatchNmax 5 -1 5 5 |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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143 --peOverlapNbasesMin 12 |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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144 --peOverlapMMp 0.1 |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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145 --chimMultimapScoreRange 10 |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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146 --chimMultimapNmax 10 |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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147 --chimNonchimScoreDropMin 10 |
22
980d2a2e1180
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
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148 |
980d2a2e1180
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
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149 #elif str( $algo.params.settingsType ) == 'arriba': |
980d2a2e1180
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
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150 ## Preset parameters for Arriba |
980d2a2e1180
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
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151 --peOverlapNbasesMin 10 |
980d2a2e1180
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
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152 --alignSplicedMateMapLminOverLmate 0.5 |
980d2a2e1180
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
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153 --alignSJstitchMismatchNmax 5 -1 5 5 |
980d2a2e1180
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
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154 --chimSegmentMin 10 |
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155 --chimJunctionOverhangMin 10 |
980d2a2e1180
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
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156 --chimScoreDropMax 30 |
980d2a2e1180
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
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157 --chimScoreJunctionNonGTAG 0 |
980d2a2e1180
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
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158 --chimScoreSeparation 1 |
980d2a2e1180
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
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159 --chimSegmentReadGapMax 3 |
980d2a2e1180
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
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160 --chimMultimapNmax 50 |
3
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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161 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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162 #elif str( $algo.params.settingsType ) == 'full': |
3
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163 ## Extended parameter options |
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164 |
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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165 ## Seed parameter options |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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166 --seedSearchStartLmax ${algo.params.seed.seedSearchStartLmax} |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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167 --seedSearchStartLmaxOverLread ${algo.params.seed.seedSearchStartLmaxOverLread} |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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168 --seedSearchLmax ${algo.params.seed.seedSearchLmax} |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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169 --seedMultimapNmax ${algo.params.seed.seedMultimapNmax} |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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170 --seedPerReadNmax ${algo.params.seed.seedPerReadNmax} |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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171 --seedPerWindowNmax ${algo.params.seed.seedPerWindowNmax} |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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172 --seedNoneLociPerWindow ${algo.params.seed.seedNoneLociPerWindow} |
9
0a563fd2f22e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7
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173 |
3
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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174 ## Alignment parameter options |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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175 --alignIntronMin ${algo.params.align.alignIntronMin} |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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176 --alignIntronMax ${algo.params.align.alignIntronMax} |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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177 --alignMatesGapMax ${algo.params.align.alignMatesGapMax} |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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178 --alignSJoverhangMin ${algo.params.align.alignSJoverhangMin} |
22
980d2a2e1180
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
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179 --alignSJstitchMismatchNmax ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax1} ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax2} ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax3} ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax4} |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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180 --alignSJDBoverhangMin ${algo.params.align.alignSJDBoverhangMin} |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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181 --alignSplicedMateMapLmin ${algo.params.align.alignSplicedMateMapLmin} |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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182 --alignSplicedMateMapLminOverLmate ${algo.params.align.alignSplicedMateMapLminOverLmate} |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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183 --alignWindowsPerReadNmax ${algo.params.align.alignWindowsPerReadNmax} |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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184 --alignTranscriptsPerWindowNmax ${algo.params.align.alignTranscriptsPerWindowNmax} |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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185 --alignTranscriptsPerReadNmax ${algo.params.align.alignTranscriptsPerReadNmax} |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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186 --alignEndsType ${algo.params.align.alignEndsType} |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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187 --peOverlapNbasesMin ${algo.params.align.peOverlapNbasesMin} |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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188 --peOverlapMMp ${algo.params.align.peOverlapMMp} |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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189 ## Chimeric alignment parameter options |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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190 #if str($chimOutType): |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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191 --chimSegmentMin ${algo.params.chim_settings.chimSegmentMin} |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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192 --chimScoreMin ${algo.params.chim_settings.chimScoreMin} |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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193 --chimScoreDropMax $algo.params.chim_settings.chimScoreDropMax |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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194 --chimScoreSeparation $algo.params.chim_settings.chimScoreSeparation |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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195 --chimScoreJunctionNonGTAG $algo.params.chim_settings.chimScoreJunctionNonGTAG |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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196 --chimSegmentReadGapMax $algo.params.chim_settings.chimSegmentReadGapMax |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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197 --chimFilter $algo.params.chim_settings.chimFilter |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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198 --chimJunctionOverhangMin $algo.params.chim_settings.chimJunctionOverhangMin |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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199 --chimMainSegmentMultNmax $algo.params.chim_settings.chimMainSegmentMultNmax |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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200 #if str($chimOutType) == 'Junctions': |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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201 --chimMultimapNmax $algo.params.chim_settings.chimMultimapNmax |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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202 #else: |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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203 --chimMultimapNmax 0 |
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0a563fd2f22e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7
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204 #end if |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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205 --chimMultimapScoreRange $algo.params.chim_settings.chimMultimapScoreRange |
3
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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206 #end if |
5
99b17b74a8cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 528ca3b14c2ca9b7ac18a0f9d80a5f4a235707bf
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207 |
99b17b74a8cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 528ca3b14c2ca9b7ac18a0f9d80a5f4a235707bf
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208 ## Limits |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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209 @LIMITS@ |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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210 #else: |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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211 ## Go with STAR's default algorithmic settings, |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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212 ## but we need to provide a reasonable default |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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213 ## (taken from STAR-Fusion) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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214 ## for --chimSegmentMin in case the user enabled chimeric |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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215 ## alignments (the STAR default is 0, which disables chimeric |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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216 ## alignments). For consistency, also set |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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217 ## --chimMultimapNmax to 1 when chimeric alignments are reported |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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218 ## in Junctions format only. |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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219 #if str($chimOutType): |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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220 --chimSegmentMin 12 |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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221 #if str($chimOutType) == 'Junctions': |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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222 --chimMultimapNmax 1 |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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223 #end if |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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224 #end if |
2
ace9f5a2b40f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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225 #end if |
ace9f5a2b40f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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226 |
10
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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227 --outBAMsortingThreadN \${GALAXY_SLOTS:-4} |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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228 --outBAMsortingBinsN $perf.outBAMsortingBinsN |
19
44959aa06aeb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 27ea73be9aede1e0939ecd7c5f560ac2a630869a"
iuc
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229 --winAnchorMultimapNmax $perf.winAnchorMultimapNmax |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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230 --limitBAMsortRAM \$((\${GALAXY_MEMORY_MB:-0}*1000000)) |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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231 |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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232 ## Handle chimeric options and output |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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233 #if str($chimOutType): |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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234 --chimOutType $chimOutType |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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235 #if 'Junctions' in str($chimOutType): |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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236 --chimOutJunctionFormat 1 |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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237 #end if |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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238 #end if |
23
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
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239 |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
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240 ##outWig: |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
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241 @OUTWIG@ |
3
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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242 && |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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243 ## recompress BAM output for smaller file size |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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244 samtools view -b -o '$mapped_reads' Aligned.sortedByCoord.out.bam |
23
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
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245 #if 'TranscriptomeSAM' in str($refGenomeSource.GTFconditional.quantmode_output.quantMode): |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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246 ## same recompression for optional transcriptome BM |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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247 && |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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248 samtools view -b -o '$transcriptome_mapped_reads' Aligned.toTranscriptome.out.bam |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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249 #end if |
23
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
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250 ##outWig: |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
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251 @OUTWIGOUTPUTS@ |
1
bc685d13b637
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 97a064489364118d108b0dd2cfb4d9bc53080837
iuc
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252 ]]></command> |
0
b2326241bb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
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253 |
b2326241bb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
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254 <inputs> |
b2326241bb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
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255 <!-- FASTQ input(s) and options specifically for paired-end data. --> |
b2326241bb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
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256 <conditional name="singlePaired"> |
2
ace9f5a2b40f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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257 <param name="sPaired" type="select" label="Single-end or paired-end reads"> |
3
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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258 <option value="single" selected="true">Single-end</option> |
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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259 <option value="paired">Paired-end (as individual datasets)</option> |
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
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260 <option value="paired_collection">Paired-end (as collection)</option> |
0
b2326241bb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
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261 </param> |
b2326241bb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
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262 <when value="single"> |
3
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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263 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" label="RNA-Seq FASTQ/FASTA file"/> |
0
b2326241bb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
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264 </when> |
b2326241bb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
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265 <when value="paired"> |
3
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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266 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" label="RNA-Seq FASTQ/FASTA file, forward reads"/> |
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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2
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267 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input2" type="data" label="RNA-Seq FASTQ/FASTA file, reverse reads"/> |
2
ace9f5a2b40f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
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268 </when> |
ace9f5a2b40f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents:
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269 <when value="paired_collection"> |
3
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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270 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input" type="data_collection" collection_type="paired" label="RNA-Seq FASTQ/FASTA paired reads"/> |
0
b2326241bb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
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271 </when> |
b2326241bb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
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272 </conditional> |
b2326241bb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
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273 |
b2326241bb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
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274 <!-- Genome source. --> |
15
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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275 <conditional name="refGenomeSource"> |
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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276 <param name="geneSource" type="select" label="Custom or built-in reference genome" help="Built-ins were indexed using default options"> |
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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277 <option value="indexed" selected="true">Use a built-in index</option> |
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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278 <option value="history">Use reference genome from history and create temporary index</option> |
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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279 </param> |
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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changeset
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280 <when value="indexed"> |
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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281 <conditional name="GTFconditional"> |
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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282 <param name="GTFselect" type="select" |
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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283 label="Reference genome with or without an annotation" |
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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284 help="Select the '... with builtin gene-model' option to select from the list of available indexes that were built with splice junction information. Select the '... without builtin gene-model' option to select from the list of available indexes without annotated splice junctions, and, optionally, provide your own splice-junction annonations."> |
23
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
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285 <option value="without-gtf-with-gtf" selected='true'>use genome reference without builtin gene-model but provide a gtf</option> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
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286 <option value="without-gtf">use genome reference without builtin gene-model and do not provide a gtf</option> |
15
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
11
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287 <option value="with-gtf">use genome reference with builtin gene-model</option> |
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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288 </param> |
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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289 <when value="with-gtf"> |
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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290 <expand macro="index_selection" with_gene_model="1" /> |
23
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
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291 <expand macro="quantMode" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
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292 </when> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
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293 <when value="without-gtf-with-gtf"> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
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294 <expand macro="index_selection" with_gene_model="0" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
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295 <expand macro="SJDBOPTIONS"/> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
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296 <expand macro="quantMode" /> |
15
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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297 </when> |
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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changeset
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298 <when value="without-gtf"> |
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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299 <expand macro="index_selection" with_gene_model="0" /> |
23
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
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300 <expand macro="quantModeNoGTF" /> |
15
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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301 </when> |
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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302 </conditional> |
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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303 </when> |
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
11
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changeset
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304 <when value="history"> |
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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changeset
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305 <expand macro="ref_selection" /> |
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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changeset
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306 <conditional name="GTFconditional"> |
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
11
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307 <param name="GTFselect" type="select" |
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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308 label="Build index with or without known splice junctions annotation" |
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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309 help="To build an index with known splice junctions annotated, you will have to provide a GTF or GFF3 dataset that describes the gene models (the location of genes, transcripts and exons) known for the reference genome."> |
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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310 <option value="without-gtf">build index without gene-model</option> |
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
11
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changeset
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311 <option value="with-gtf">build index with gene-model</option> |
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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changeset
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312 </param> |
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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changeset
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313 <when value="with-gtf"> |
23
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
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314 <expand macro="SJDBOPTIONS"/> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
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315 <expand macro="quantMode" /> |
15
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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316 </when> |
23
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
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changeset
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317 <when value="without-gtf"> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
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318 <expand macro="quantModeNoGTF" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
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319 </when> |
15
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
11
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changeset
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320 </conditional> |
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
11
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changeset
|
321 </when> |
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
11
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changeset
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322 </conditional> |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
323 |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
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changeset
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324 <conditional name="twopass"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
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changeset
|
325 <param argument="--twopassMode" type="select" |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
326 label="Use 2-pass mapping for more sensitive novel splice junction discovery" |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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327 help="For a study with multiple samples, multisample 2-pass mapping is the most sensitive approach. It involves two separate runs of STAR for each sample, where, in the second run of each sample, the splice junctions found in any sample in the first runs are treated as additional known junctions. If you plan to use the mapping results as input for STAR-Fusion it is recommended that you use at least single-sample 2-pass mapping of all reads."> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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328 <option value="None">No</option> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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329 <option value="Basic">Yes, perform single-sample 2-pass mapping of all reads</option> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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330 <option value="Basic --twopass1readsN">Yes, but base novel splice junction detection in the first pass on a subset of all reads (faster, but less sensitive than single-sample 2-pass mode)</option> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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331 <option value="None --sjdbFileChrStartEnd">Yes, I want to use multi-sample 2-pass mapping and I have obtained splice junctions datasets of all samples through previous 1-pass runs of STAR.</option> |
0
b2326241bb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
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332 </param> |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
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changeset
|
333 <when value="None"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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334 <param name="twopass_read_subset" type="hidden" value="" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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335 <param name="sj_precalculated" type="hidden" value="" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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336 </when> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
337 <when value="Basic"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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338 <param name="twopass_read_subset" type="hidden" value="" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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339 <param name="sj_precalculated" type="hidden" value="" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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340 </when> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
341 <when value="Basic --twopass1readsN"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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changeset
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342 <param name="sj_precalculated" type="hidden" value="" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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343 <param argument="--twopass1readsN" name="twopass_read_subset" type="integer" min="1" value="50000" label="Number of reads to map in the first pass"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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344 </when> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
345 <when value="None --sjdbFileChrStartEnd"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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346 <param name="twopass_read_subset" type="hidden" value="" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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347 <param name="sj_precalculated" type="data" multiple="true" format="interval" |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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348 label="Pregenerated splice junctions datasets of your samples" /> |
0
b2326241bb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
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349 </when> |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
350 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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351 <param argument="--chimOutType" type="select" |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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352 label="Report chimeric alignments?" |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
353 help="Choose if and how chimeric alignments should be reported. STAR-Fusion users should select the 'Junctions' option and use the resulting tabular dataset as input to STAR-Fusion. Everyone else: note that selecting 'WithinBAM' or 'WithinBAM Junctions' disables the --chimMultimapNmax setting in the algorithmic parameters section below (the tool will only consider uniquely mapped reads in the search for chimeric alignments). If you disable the reporting of chimeric alignments here, then all chimeric alignment settings in the algorithmic parameters section below will be ignored."> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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354 <option value="">Don't report chimeric alignments</option> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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355 <option value="Junctions">As separate tabular "Junctions" output (Junctions)</option> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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356 <option value="WithinBAM">Within the BAM output (together with regular alignments; WithinBAM)</option> |
22
980d2a2e1180
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
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357 <option value="WithinBAM HardClip">Within the BAM output (together with regular alignments; WithinBAM HardClip) hard-clipping in the CIGAR for supplemental chimeric alignments</option> |
980d2a2e1180
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
parents:
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358 <option value="WithinBAM SoftClip">Within the BAM output (together with regular alignments; WithinBAM SoftClip) soft-clipping in the CIGAR for supplemental chimeric alignments</option> |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
359 </param> |
9
0a563fd2f22e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7
iuc
parents:
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|
360 |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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361 <section name="oformat" title="BAM output format specification" expanded="true"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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362 <param argument="--outSAMattributes" type="select" display="checkboxes" multiple="true" optional="true" |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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changeset
|
363 label="Read alignment tags to include in the BAM output" |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
364 help="Note on using the XS tag: If the XS tag is used, STAR will filter out alignments with undefined strand (i.e., those containing only non-canonical unannotated junctions). Using this tag is recommended if you plan to use the STAR results with STAR-Fusion. In addition, it is required for compatibility |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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diff
changeset
|
365 with Cufflinks if your sequences come from an unstranded library preparation."> |
23
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
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|
366 <expand macro="common_SAM_attributes"/> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
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367 <option value="MC">MC (CIGAR string for mate/next segment)</option> |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
368 <option value="XS">XS (strand flag, see parameter help below) </option> |
23
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
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369 <option value="ch" selected="true">ch (used to indicate chimeric alignments)</option> <!--This is not the default in STAR--> |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
370 </param> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
371 <param argument="--outSAMattrIHstart" name="HI_offset" type="select" display="radio" |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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changeset
|
372 label="HI tag values should be"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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373 <option value="1" selected="true">one-based</option> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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374 <option value="0">zero-based</option> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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375 </param> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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376 <!-- Using - -outSAMprimaryFlag AllBestScore would cause a |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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377 violation of the SAM/BAM spec, which says: |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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378 "For each read/contig in a SAM file, it is required that one and |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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379 only one line associated with the read satisfies |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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380 ‘FLAG & 0x900 == 0’. |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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381 This line is called the primary line of the read." |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
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382 |
10
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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383 Thus, this parameter has been removed from the tool interface: |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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384 <param argument="- -outSAMprimaryFlag" type="boolean" |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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385 truevalue="AllBestScore" falsevalue="OneBestScore" checked="false" |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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386 label="Would you like all alignments with the best score labeled |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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387 primary?"/> --> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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388 <param name="outSAMprimaryFlag" type="hidden" value="OneBestScore" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
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389 <expand macro="outSAMmapqUnique"/> |
10
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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390 </section> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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391 <section name="filter" title="Output filter criteria" expanded="true"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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392 <param name="basic_filters" type="select" display="checkboxes" multiple="true" optional="true" |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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393 label="Exclude the following records from the BAM output"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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394 <option value="exclude_unmapped">Unmapped reads</option> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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395 <option value="--outFilterIntronStrands RemoveInconsistentStrands">Alignments that have junctions with inconsistent strands</option> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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396 <option value="--outFilterIntronMotifs RemoveNoncanonicalUnannotated">Alignments across unannotated non-canonical junctions</option> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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397 <option value="--outFilterIntronMotifs RemoveNoncanonical">All alignments across non-canonical junctions (recommended for compatibility with Cufflinks)</option> |
3
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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398 </param> |
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d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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399 <!-- Additional output parameter settings. --> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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400 <conditional name="output_params2"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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401 <param name="output_select2" type="select" label="Would you like to set additional output filters?"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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402 <option value="no" selected="true">No</option> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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403 <option value="yes">Yes</option> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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404 </param> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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405 <when value="yes"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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406 <param argument="--outFilterType" type="boolean" truevalue="BySJout" falsevalue="Normal" checked="false" label="Would you like to keep only reads that contain junctions that passed filtering?"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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407 <param argument="--outFilterMultimapScoreRange" type="integer" value="1" min="0" label="Score range below the maximum score for multimapping alignments"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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408 <param argument="--outFilterMultimapNmax" type="integer" value="10" min="1" label="Maximum number of alignments to output a read's alignment results, plus 1" help="Reads with at least this number of alignments will have no alignments output"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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409 <param argument="--outFilterMismatchNmax" type="integer" value="10" min="0" label="Maximum number of mismatches to output an alignment, plus 1" help="Alignments with at least this number of mismatches will not be output"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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410 <param argument="--outFilterMismatchNoverLmax" type="float" value="0.3" min="0" max="1" label="Maximum ratio of mismatches to mapped length" help="Alignments with a mismatch ratio of at least this value will not be output"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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411 <param argument="--outFilterMismatchNoverReadLmax" type="float" value="1" min="0" max="1" label="Maximum ratio of mismatches to read length" help="Alignments with a mismatch ratio of at least this value will not be output"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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412 <param argument="--outFilterScoreMin" type="integer" value="0" min="0" label="Minimum alignment score" help="Alignments must have scores higher than this value to be output"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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413 <param argument="--outFilterScoreMinOverLread" type="float" value="0.66" min="0" max="1" label="Minimum alignment score, normalized to read length" help="Alignments must have (normalized) scores higher than this value to be output"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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414 <param argument="--outFilterMatchNmin" type="integer" value="0" min="0" label="Minimum number of matched bases" help="Alignments must have the number of matched bases higher than this value to be output"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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415 <param argument="--outFilterMatchNminOverLread" type="float" value="0.66" min="0" max="1" label="Minimum number of matched bases, normalized to read length" help="Alignments must have the (normalized) number of matched bases higher than this value to be output"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
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416 <param argument="--outSAMmultNmax" type="integer" value="-1" min="-1" label="Maximum number of multimapping alignments to output for a read" help="A value of -1 (the default) results in all alignments (up to --outFilterMultimapNmax) being output" /> |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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417 <param argument="--outSAMtlen" type="select" label="Calculation method for TLEN"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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418 <option value="1" selected="true">leftmost base of the (+)strand mate to rightmost base of the (-)mate. (+)sign for the (+)strand mate</option> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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419 <option value="2">leftmost base of any mate to rightmost base of any mate. (+)sign for the mate with the leftmost base. This is different from 1 for overlapping mates with protruding ends</option> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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420 </param> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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421 </when> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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422 <when value="no"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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423 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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424 </section> |
9
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7
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425 |
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d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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426 <!-- Algorithmic settings. --> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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427 <section name="algo" title="Algorithmic settings" expanded="true"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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428 <conditional name="params"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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429 <param name="settingsType" type="select" label="Configure seed, alignment and limits options"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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430 <option value="default" selected="true">Use Defaults</option> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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431 <option value="star_fusion">Use parameters suggested for STAR-Fusion</option> |
22
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
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432 <option value="arriba">Use parameters suggested for Arriba</option> |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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433 <option value="full">Extended parameter list</option> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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434 </param> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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435 <when value="default"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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436 <!-- Set STAR-fusion parameters in command section --> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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437 <when value="star_fusion"/> |
22
980d2a2e1180
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
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438 <when value="arriba"/> |
5
99b17b74a8cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 528ca3b14c2ca9b7ac18a0f9d80a5f4a235707bf
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439 |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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440 <when value="full"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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441 <section name="seed" title="Seed parameters" expanded="false"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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442 <param argument="--seedSearchStartLmax" type="integer" min="1" value="50" label="Search start point through the read"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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443 <param argument="--seedSearchStartLmaxOverLread" type="float" min="0" value="1.0" label="Search start point through the read, normalized to read length"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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444 <param argument="--seedSearchLmax" type="integer" min="0" value="0" label="Maximum length of seeds" help="Default of 0 indicates no maximum length"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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|
445 <param argument="--seedMultimapNmax" type="integer" min="1" value="10000" label="Maximum number of mappings to use a piece in stitching"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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changeset
|
446 <param argument="--seedPerReadNmax" type="integer" min="1" value="1000" label="Maximum number of seeds per read"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
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changeset
|
447 <param argument="--seedPerWindowNmax" type="integer" min="1" value="50" label="Maximum number of seeds per window"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
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changeset
|
448 <param argument="--seedNoneLociPerWindow" type="integer" min="1" value="10" label="Maximum number of one seed loci per window"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
449 </section> |
9
0a563fd2f22e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7
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parents:
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changeset
|
450 |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
451 <section name="align" title="Alignment parameters" expanded="false"> |
23
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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parents:
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|
452 <param argument="--alignIntronMin" type="integer" min="0" value="21" label="Minimum intron size"/> |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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changeset
|
453 <param argument="--alignIntronMax" type="integer" min="0" value="0" label="Maximum intron size"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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changeset
|
454 <param argument="--alignMatesGapMax" type="integer" min="0" value="0" label="Maximum gap between two mates"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
455 <param argument="--alignSJoverhangMin" type="integer" min="1" value="5" label="Minimum overhang for spliced alignments"/> |
22
980d2a2e1180
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
parents:
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|
456 <section name="alignSJstitchMismatchNmax" title="Maximum number of mismatches for stitching of the splice junctions (-1: no limit)" expanded="true"> |
980d2a2e1180
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
parents:
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|
457 <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax1" type="integer" min="-1" value="0" label="Non-canonical motifs"/> |
980d2a2e1180
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
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|
458 <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax2" type="integer" min="-1" value="-1" label="GT/AG and CT/AC motif"/> |
980d2a2e1180
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
parents:
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|
459 <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax3" type="integer" min="-1" value="0" label="GC/AG and CT/GC motif"/> |
980d2a2e1180
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
parents:
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460 <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax4" type="integer" min="-1" value="0" label="AT/AC and GT/AT motif"/> |
980d2a2e1180
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
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|
461 </section> |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
462 <param argument="--alignSJDBoverhangMin" type="integer" min="1" value="3" label="Minimum overhang for annotated spliced alignments"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
463 <param argument="--alignSplicedMateMapLmin" type="integer" min="0" value="0" label="Minimum mapped length for a read mate that is spliced"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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|
464 <param argument="--alignSplicedMateMapLminOverLmate" type="float" min="0" value="0.66" label="Minimum mapped length for a read mate that is spliced, normalized to mate length"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
465 <param argument="--alignWindowsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of windows per read"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
466 <param argument="--alignTranscriptsPerWindowNmax" type="integer" min="1" value="100" label="Maximum number of transcripts per window"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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|
467 <param argument="--alignTranscriptsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of different alignments per read to consider"/> |
23
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
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468 <param argument="--alignEndsType" type="select" label="type of read ends alignment"> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
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469 <option value="Local">standard local alignment with soft-clipping allowed</option> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
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470 <option value="EndToEnd">force end-to-end read alignment, do not soft-clip</option> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
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changeset
|
471 <option value="Extend5pOfRead1">fully extend only the 5p of the read1, all other ends: local alignment</option> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
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changeset
|
472 <option value="Extend5pOfReads12">fully extend only the 5p of the both read1 and read2, all other ends: local alignment</option> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
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|
473 </param> |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
474 <param argument="--peOverlapNbasesMin" type="integer" min="0" value="0" |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
475 label="minimum number of overlap bases to trigger mates merging and realignment" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
476 <param argument="--peOverlapMMp" type="float" min="0" max="1" value="0.01" |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
477 label="maximum proportion of mismatched bases in the overlap area" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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478 </section> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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|
479 <section name="chim_settings" title="Chimeric alignment parameters" expanded="false"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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|
480 <param argument="--chimSegmentMin" type="integer" min="1" value="12" |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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|
481 label="Minimum length of chimeric segment" |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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482 help="For small numbers this will cause large number of chimeric alignments. A value of 12 is commonly used." /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
483 <param argument="--chimScoreMin" type="integer" min="0" value="0" |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
484 label="Minimum total (summed) score of chimeric segments"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
485 <param argument="--chimScoreDropMax" type="integer" min="0" value="20" |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
486 label="Maximum difference of chimeric score from read length"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
487 <param argument="--chimScoreSeparation" type="integer" min="0" value="10" |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
488 label="Minimum difference between the best chimeric score and the next one"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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489 <param argument="--chimScoreJunctionNonGTAG" type="integer" value="-1" |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
490 label="Penalty for a non-GT/AG chimeric junction"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
491 <param argument="--chimJunctionOverhangMin" type="integer" min="0" value="20" |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
492 label="Minimum overhang for a chimeric junction"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
493 <param argument="--chimSegmentReadGapMax" type="integer" min="0" value="0" |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
494 label="Maximum gap in the read sequence between chimeric segments" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
495 <param argument="--chimFilter" type="boolean" truevalue="banGenomicN" falsevalue="None" checked="true" |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
496 label="Discard chimeric alignments with Ns in the genome sequence around the chimeric junction" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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|
497 <param argument="--chimMainSegmentMultNmax" type="integer" min="1" value="10" |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
498 label="Maximum number of multi-alignments for the main chimeric segment." |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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|
499 help="A value of 1 prohibits multimapping main segments"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
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|
500 <param argument="--chimMultimapNmax" type="integer" min="1" value="1" |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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changeset
|
501 label="Maximum number of chimeric multi-alignments" |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
502 help="The default value of 1 only considers unique alignments. If you chose to report chimeric alignments alongside regular ones in the BAM output, this setting is ignored and only uniquely mapping chimeric reads get reported. " /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
503 <param argument="--chimMultimapScoreRange" type="integer" min="0" value="1" |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
504 label="Score range for multi-mapping chimeras" |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
505 help="The threshold below the best chimeric score that a multimapping chimera must have to be output. This is ignored unless --chimMultimapNmax is above 1" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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|
506 </section> |
23
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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|
507 <expand macro="limits" /> |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
508 </when> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
509 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
510 </section> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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changeset
|
511 <section name="perf" title="Performance tweaks / Troubleshooting" expanded="false"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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|
512 <param argument="--outBAMsortingBinsN" type="integer" value="50" min="1" label="Number of genome bins for coordinate-sorting" help="Higher values result in lower RAM requirements during the sorting step. The default value is 50. Tweak this if you are facing memory-related errors." /> |
19
44959aa06aeb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 27ea73be9aede1e0939ecd7c5f560ac2a630869a"
iuc
parents:
18
diff
changeset
|
513 <param argument="--winAnchorMultimapNmax" type="integer" value="50" min="50" label="Maximum number of loci anchors are allowed to map to" help="Higher value can increase the runtime singificantly. This value should be set greater or equal to --outFilterMultimapNmax" /> |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
514 </section> |
23
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
515 <expand macro="outWig"/> |
0
b2326241bb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff
changeset
|
516 </inputs> |
b2326241bb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff
changeset
|
517 |
b2326241bb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff
changeset
|
518 <outputs> |
8
d5659efd66aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167
iuc
parents:
7
diff
changeset
|
519 <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out"> |
d5659efd66aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167
iuc
parents:
7
diff
changeset
|
520 <expand macro="dbKeyActions" /> |
d5659efd66aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167
iuc
parents:
7
diff
changeset
|
521 </data> |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
522 |
3
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
2
diff
changeset
|
523 <data format="interval" name="chimeric_junctions" label="${tool.name} on ${on_string}: chimeric junctions" from_work_dir="Chimeric.out.junction"> |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
524 <filter>('Junctions' in chimOutType)</filter> |
8
d5659efd66aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167
iuc
parents:
7
diff
changeset
|
525 <expand macro="dbKeyActions" /> |
3
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
2
diff
changeset
|
526 </data> |
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
2
diff
changeset
|
527 |
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
2
diff
changeset
|
528 <data format="interval" name="splice_junctions" label="${tool.name} on ${on_string}: splice junctions.bed" from_work_dir="SJ.out.tab"> |
8
d5659efd66aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167
iuc
parents:
7
diff
changeset
|
529 <expand macro="dbKeyActions" /> |
3
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
2
diff
changeset
|
530 </data> |
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
2
diff
changeset
|
531 |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
532 <data name="mapped_reads" format="bam" label="${tool.name} on ${on_string}: mapped.bam"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
533 <expand macro="dbKeyActions" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
534 </data> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
535 |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
536 <data name="transcriptome_mapped_reads" format="unsorted.bam" label="${tool.name} on ${on_string}: transcriptome-mapped.bam" > |
23
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
537 <filter>'TranscriptomeSAM' in refGenomeSource['GTFconditional']['quantmode_output']['quantMode']</filter> |
8
d5659efd66aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167
iuc
parents:
7
diff
changeset
|
538 <expand macro="dbKeyActions" /> |
0
b2326241bb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff
changeset
|
539 </data> |
9
0a563fd2f22e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7
iuc
parents:
8
diff
changeset
|
540 |
3
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
2
diff
changeset
|
541 <data name="reads_per_gene" format="tabular" label="${tool.name} on ${on_string}: reads per gene" from_work_dir="ReadsPerGene.out.tab"> |
23
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
542 <filter>'GeneCounts' in refGenomeSource['GTFconditional']['quantmode_output']['quantMode']</filter> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
543 <expand macro="outCountActions" /> |
0
b2326241bb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff
changeset
|
544 </data> |
23
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
545 <expand macro="outWigOutputs"/> |
0
b2326241bb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff
changeset
|
546 </outputs> |
2
ace9f5a2b40f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents:
1
diff
changeset
|
547 |
0
b2326241bb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff
changeset
|
548 <tests> |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
549 <test expect_num_outputs="3"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
550 <conditional name="singlePaired"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
551 <param name="sPaired" value="single" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
552 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
553 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
554 <conditional name="refGenomeSource"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
555 <param name="geneSource" value="history" /> |
23
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
556 <param name="genomeFastaFiles" value="tophat_test.fa.gz" /> |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
557 <param name="genomeSAindexNbases" value="5" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
558 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
559 <section name="oformat"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
560 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
561 </section> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
562 <section name="algo"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
563 <conditional name="params"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
564 <param name="settingsType" value="default" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
565 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
566 </section> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
567 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" /> |
2
ace9f5a2b40f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents:
1
diff
changeset
|
568 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/> |
3
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
2
diff
changeset
|
569 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" /> |
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
2
diff
changeset
|
570 </test> |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
571 <!-- test with cached genome index --> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
572 <test expect_num_outputs="3"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
573 <conditional name="singlePaired"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
574 <param name="sPaired" value="single" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
575 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
576 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
577 <conditional name="refGenomeSource"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
578 <param name="geneSource" value="indexed" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
579 <conditional name="GTFconditional"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
580 <param name="GTFselect" value="with-gtf" /> |
11
41929aa1e7f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2911002ccd79fe062f6346ee5699ea262f92f04f"
iuc
parents:
10
diff
changeset
|
581 <param name="genomeDir" value="001" /> |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
582 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
583 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
584 <section name="oformat"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
585 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
586 </section> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
587 <section name="algo"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
588 <conditional name="params"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
589 <param name="settingsType" value="default" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
590 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
591 </section> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
592 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
593 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
594 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
595 </test> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
596 <!-- test gtf file and GeneCounts mode --> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
597 <test expect_num_outputs="4"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
598 <conditional name="singlePaired"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
599 <param name="sPaired" value="single" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
600 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
601 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
602 <conditional name="refGenomeSource"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
603 <param name="geneSource" value="history" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
604 <param name="genomeFastaFiles" value="tophat_test.fa" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
605 <param name="genomeSAindexNbases" value="5" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
606 <conditional name="GTFconditional"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
607 <param name="GTFselect" value="with-gtf" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
608 <param name="sjdbOverhang" value="75"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
609 <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/> |
23
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
610 <conditional name="quantmode_output"> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
611 <param name="quantMode" value="GeneCounts"/> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
612 </conditional> |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
613 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
614 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
615 <section name="oformat"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
616 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
617 </section> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
618 <section name="algo"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
619 <conditional name="params"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
620 <param name="settingsType" value="default" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
621 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
622 </section> |
3
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
2
diff
changeset
|
623 |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
624 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" /> |
3
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
2
diff
changeset
|
625 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/> |
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
2
diff
changeset
|
626 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" /> |
24
4df95e2d7f61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents:
23
diff
changeset
|
627 <output name="reads_per_gene" file="tophat_test_reads_per_gene.txt"> |
4df95e2d7f61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents:
23
diff
changeset
|
628 <metadata name="column_names" value="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand" /> |
4df95e2d7f61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents:
23
diff
changeset
|
629 </output> |
1
bc685d13b637
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 97a064489364118d108b0dd2cfb4d9bc53080837
iuc
parents:
0
diff
changeset
|
630 </test> |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
631 <!-- test gtf file and TranscriptomeSAM mode --> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
632 <test expect_num_outputs="4"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
633 <conditional name="singlePaired"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
634 <param name="sPaired" value="single" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
635 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
636 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
637 <conditional name="refGenomeSource"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
638 <param name="geneSource" value="history" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
639 <param name="genomeFastaFiles" value="tophat_test.fa" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
640 <param name="genomeSAindexNbases" value="5" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
641 <conditional name="GTFconditional"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
642 <param name="GTFselect" value="with-gtf" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
643 <param name="sjdbOverhang" value="75"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
644 <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/> |
23
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
645 <conditional name="quantmode_output"> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
646 <param name="quantMode" value="TranscriptomeSAM"/> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
647 </conditional> |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
648 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
649 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
650 <section name="oformat"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
651 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
652 </section> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
653 <section name="algo"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
654 <conditional name="params"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
655 <param name="settingsType" value="default" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
656 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
657 </section> |
9
0a563fd2f22e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7
iuc
parents:
8
diff
changeset
|
658 |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
659 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
660 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
661 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" /> |
22
980d2a2e1180
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
parents:
20
diff
changeset
|
662 <output name="transcriptome_mapped_reads" file="rnastar_test_transcriptome_mapped_reads.bam" compare="sim_size" delta="634" /> |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
663 </test> |
23
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
664 <!-- test cached no index but gtf file and GeneCounts TranscriptomeSAM mode --> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
665 <test expect_num_outputs="5"> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
666 <conditional name="singlePaired"> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
667 <param name="sPaired" value="single" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
668 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
669 </conditional> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
670 <conditional name="refGenomeSource"> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
671 <param name="geneSource" value="indexed" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
672 <conditional name="GTFconditional"> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
673 <param name="GTFselect" value="without-gtf-with-gtf" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
674 <param name="genomeDir" value="000" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
675 <param name="sjdbOverhang" value="75"/> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
676 <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
677 <conditional name="quantmode_output"> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
678 <param name="quantMode" value="TranscriptomeSAM GeneCounts"/> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
679 </conditional> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
680 </conditional> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
681 </conditional> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
682 <section name="oformat"> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
683 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
684 </section> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
685 <section name="algo"> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
686 <conditional name="params"> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
687 <param name="settingsType" value="default" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
688 </conditional> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
689 </section> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
690 |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
691 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
692 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
693 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
694 <output name="reads_per_gene" file="tophat_test_reads_per_gene.txt" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
695 <output name="transcriptome_mapped_reads" file="rnastar_test_transcriptome_mapped_reads.bam" compare="sim_size" delta="634" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
696 </test> |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
697 <test expect_num_outputs="3"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
698 <conditional name="singlePaired"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
699 <param name="sPaired" value="single" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
700 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
701 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
702 <conditional name="refGenomeSource"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
703 <param name="geneSource" value="history" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
704 <param name="genomeFastaFiles" value="tophat_test.fa" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
705 <param name="genomeSAindexNbases" value="5" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
706 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
707 <section name="oformat"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
708 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch,XS" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
709 </section> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
710 <section name="filter"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
711 <param name="basic_filters" value="exclude_unmapped,--outFilterIntronMotifs RemoveNoncanonical" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
712 <conditional name="output_params2"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
713 <param name="output_select2" value="yes" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
714 <param name="outFilterScoreMinOverLread" value="0.9" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
715 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
716 </section> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
717 <section name="algo"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
718 <conditional name="params"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
719 <param name="settingsType" value="full" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
720 <section name="seed"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
721 <param name="seed_select" value="yes" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
722 <param name="seedSearchStartLmax" value="25" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
723 </section> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
724 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
725 </section> |
9
0a563fd2f22e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7
iuc
parents:
8
diff
changeset
|
726 |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
727 <output name="output_log" file="rnastar_test2.log" compare="re_match_multiline" /> |
2
ace9f5a2b40f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents:
1
diff
changeset
|
728 <output name="splice_junctions" file="rnastar_test2_splicejunctions.bed"/> |
ace9f5a2b40f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents:
1
diff
changeset
|
729 <output name="mapped_reads" file="rnastar_test2_mapped_reads.bam" compare="sim_size" delta="200" /> |
0
b2326241bb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff
changeset
|
730 </test> |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
731 <test expect_num_outputs="4"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
732 <conditional name="singlePaired"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
733 <param name="sPaired" value="single" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
734 <param name="input1" value="test3.fastqsanger" ftype="fastqsanger" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
735 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
736 <conditional name="refGenomeSource"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
737 <param name="geneSource" value="history" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
738 <param name="genomeFastaFiles" value="test3.ref.fa" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
739 <param name="genomeSAindexNbases" value="5" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
740 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
741 <param name="chimOutType" value="Junctions" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
742 <section name="oformat"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
743 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch,XS" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
744 </section> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
745 <section name="algo"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
746 <conditional name="params"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
747 <param name="settingsType" value="star_fusion" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
748 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
749 </section> |
3
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
2
diff
changeset
|
750 |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
751 <output name="chimeric_junctions" file="test3.chimjunc.tabular" compare="diff" lines_diff="2"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
752 </test> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
753 <test expect_num_outputs="4"><!-- tests fastqsanger.gz --> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
754 <conditional name="singlePaired"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
755 <param name="sPaired" value="single" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
756 <param name="input1" value="test3.fastqsanger.gz" ftype="fastqsanger.gz" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
757 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
758 <conditional name="refGenomeSource"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
759 <param name="geneSource" value="history" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
760 <param name="genomeFastaFiles" value="test3.ref.fa" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
761 <param name="genomeSAindexNbases" value="5" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
762 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
763 <param name="chimOutType" value="Junctions" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
764 <section name="oformat"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
765 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch,XS" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
766 </section> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
767 <section name="algo"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
768 <conditional name="params"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
769 <param name="settingsType" value="star_fusion" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
770 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
771 </section> |
3
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
2
diff
changeset
|
772 |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
773 <output name="chimeric_junctions" file="test3.chimjunc.tabular" compare="diff" lines_diff="2"/> |
3
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
2
diff
changeset
|
774 </test> |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
775 <test expect_num_outputs="3"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
776 <conditional name="singlePaired"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
777 <param name="sPaired" value="single" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
778 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
779 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
780 <conditional name="refGenomeSource"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
781 <param name="geneSource" value="history" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
782 <param name="genomeFastaFiles" value="tophat_test.fa" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
783 <param name="genomeSAindexNbases" value="5" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
784 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
785 <section name="oformat"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
786 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
787 </section> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
788 <section name="filter"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
789 <param name="basic_filters" value="--outFilterIntronMotifs RemoveNoncanonical" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
790 <conditional name="output_params2"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
791 <param name="output_select2" value="yes" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
792 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
793 </section> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
794 <section name="algo"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
795 <conditional name="params"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
796 <param name="settingsType" value="full" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
797 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
798 </section> |
3
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
2
diff
changeset
|
799 |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
800 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" /> |
2
ace9f5a2b40f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents:
1
diff
changeset
|
801 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/> |
3
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
2
diff
changeset
|
802 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" /> |
2
ace9f5a2b40f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents:
1
diff
changeset
|
803 </test> |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
804 <!-- twopass mode tests --> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
805 <!-- test Basic twopass --> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
806 <test expect_num_outputs="3"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
807 <conditional name="singlePaired"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
808 <param name="sPaired" value="single" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
809 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
810 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
811 <conditional name="refGenomeSource"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
812 <param name="geneSource" value="history" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
813 <param name="genomeFastaFiles" value="tophat_test.fa" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
814 <param name="genomeSAindexNbases" value="5" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
815 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
816 <conditional name="twopass"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
817 <param name="twopassMode" value="Basic" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
818 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
819 <section name="oformat"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
820 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
821 </section> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
822 <section name="filter"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
823 <param name="basic_filters" value="exclude_unmapped,--outFilterIntronMotifs RemoveNoncanonical" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
824 <conditional name="output_params2"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
825 <param name="output_select2" value="yes" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
826 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
827 </section> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
828 <section name="algo"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
829 <conditional name="params"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
830 <param name="settingsType" value="full" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
831 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
832 </section> |
9
0a563fd2f22e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7
iuc
parents:
8
diff
changeset
|
833 |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
834 <output name="output_log" file="rnastar_test_twopass.log" compare="re_match_multiline" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
835 <output name="splice_junctions" file="rnastar_test_splicejunctions_twopass.bed"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
836 <output name="mapped_reads" file="rnastar_test_mapped_reads_twopass.bam" compare="sim_size" delta="634" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
837 </test> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
838 <!-- test Basic twopass without a gtf file option --> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
839 <test expect_num_outputs="3"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
840 <conditional name="singlePaired"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
841 <param name="sPaired" value="single" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
842 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
843 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
844 <conditional name="refGenomeSource"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
845 <param name="geneSource" value="indexed" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
846 <conditional name="GTFconditional"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
847 <param name="GTFselect" value="without-gtf" /> |
11
41929aa1e7f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2911002ccd79fe062f6346ee5699ea262f92f04f"
iuc
parents:
10
diff
changeset
|
848 <param name="genomeDir" value="000" /> |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
849 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
850 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
851 <conditional name="twopass"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
852 <param name="twopassMode" value="Basic" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
853 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
854 <section name="oformat"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
855 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
856 </section> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
857 <section name="filter"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
858 <param name="basic_filters" value="exclude_unmapped,--outFilterIntronMotifs RemoveNoncanonical" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
859 <conditional name="output_params2"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
860 <param name="output_select2" value="yes" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
861 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
862 </section> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
863 <section name="algo"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
864 <conditional name="params"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
865 <param name="settingsType" value="full" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
866 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
867 </section> |
9
0a563fd2f22e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7
iuc
parents:
8
diff
changeset
|
868 |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
869 <output name="output_log" file="rnastar_test_twopass.log" compare="re_match_multiline" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
870 <output name="splice_junctions" file="rnastar_test_splicejunctions_twopass.bed"/> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
871 <output name="mapped_reads" file="rnastar_test_mapped_reads_twopass.bam" compare="sim_size" delta="634" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
872 </test> |
20
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
873 <!-- test Basic twopass with a built-in gtf index option --> |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
874 <test expect_num_outputs="3"> |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
875 <conditional name="singlePaired"> |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
876 <param name="sPaired" value="single" /> |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
877 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" /> |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
878 </conditional> |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
879 <conditional name="refGenomeSource"> |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
880 <param name="geneSource" value="indexed" /> |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
881 <conditional name="GTFconditional"> |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
882 <param name="GTFselect" value="with-gtf" /> |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
883 <param name="genomeDir" value="001" /> |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
884 </conditional> |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
885 </conditional> |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
886 <conditional name="twopass"> |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
887 <param name="twopassMode" value="Basic" /> |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
888 </conditional> |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
889 <section name="oformat"> |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
890 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
891 </section> |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
892 <section name="filter"> |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
893 <param name="basic_filters" value="exclude_unmapped,--outFilterIntronMotifs RemoveNoncanonical" /> |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
894 <conditional name="output_params2"> |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
895 <param name="output_select2" value="yes" /> |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
896 </conditional> |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
897 </section> |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
898 <section name="algo"> |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
899 <conditional name="params"> |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
900 <param name="settingsType" value="full" /> |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
901 </conditional> |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
902 </section> |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
903 |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
904 <output name="output_log" file="rnastar_test_twopass.log" compare="re_match_multiline" /> |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
905 <output name="splice_junctions" file="rnastar_test_splicejunctions_twopass.bed"/> |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
906 <output name="mapped_reads" file="rnastar_test_mapped_reads_twopass.bam" compare="sim_size" delta="634" /> |
91e0f03268ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit c1bd0c35d60419e2b45d29b0705b9efac8908011"
iuc
parents:
19
diff
changeset
|
907 </test> |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
908 <!-- test "multisample" twopass --> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
909 <test expect_num_outputs="3"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
910 <conditional name="singlePaired"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
911 <param name="sPaired" value="single" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
912 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
913 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
914 <conditional name="refGenomeSource"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
915 <param name="geneSource" value="history" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
916 <param name="genomeFastaFiles" value="tophat_test.fa" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
917 <param name="genomeSAindexNbases" value="5" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
918 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
919 <conditional name="twopass"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
920 <param name="twopassMode" value="None --sjdbFileChrStartEnd" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
921 <param name="sj_precalculated" value="rnastar_test_splicejunctions_twopass.bed" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
922 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
923 <section name="oformat"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
924 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
925 </section> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
926 <section name="filter"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
927 <param name="basic_filters" value="exclude_unmapped,--outFilterIntronMotifs RemoveNoncanonicalUnannotated,--outFilterIntronMotifs RemoveNoncanonical" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
928 <conditional name="output_params2"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
929 <param name="output_select2" value="yes" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
930 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
931 </section> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
932 <section name="algo"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
933 <conditional name="params"> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
934 <param name="settingsType" value="full" /> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
935 </conditional> |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
936 </section> |
9
0a563fd2f22e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7
iuc
parents:
8
diff
changeset
|
937 |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
938 <output name="output_log" file="rnastar_test_twopass.log" compare="re_match_multiline" /> |
9
0a563fd2f22e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7
iuc
parents:
8
diff
changeset
|
939 <output name="splice_junctions" file="rnastar_test_splicejunctions_twopass.bed"/> |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
940 <output name="mapped_reads" file="rnastar_test_mapped_reads_twopass.bam" compare="sim_size" delta="634" /> |
9
0a563fd2f22e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7
iuc
parents:
8
diff
changeset
|
941 </test> |
18
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
942 <!-- test "genomeSAindexNbases" parameter --> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
943 <test expect_num_outputs="3"> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
944 <conditional name="singlePaired"> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
945 <param name="sPaired" value="single" /> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
946 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" /> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
947 </conditional> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
948 <conditional name="refGenomeSource"> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
949 <param name="geneSource" value="history" /> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
950 <param name="genomeFastaFiles" value="tophat_test.fa" /> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
951 <param name="genomeSAindexNbases" value="14" /> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
952 </conditional> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
953 <section name="oformat"> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
954 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
955 </section> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
956 <section name="algo"> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
957 <conditional name="params"> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
958 <param name="settingsType" value="default" /> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
959 </conditional> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
960 </section> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
961 <output name="output_log" file="rnastar_test_genomeSAindexNbases.log" compare="re_match_multiline" /> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
962 <output name="splice_junctions" file="rnastar_test_genomeSAindexNbases.bed"/> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
963 <output name="mapped_reads" file="rnastar_test_mapped_reads_genomeSAindexNbases.bam" compare="sim_size" delta="634" /> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
964 </test> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
965 <test expect_num_outputs="3"> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
966 <conditional name="singlePaired"> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
967 <param name="sPaired" value="single" /> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
968 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" /> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
969 </conditional> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
970 <conditional name="refGenomeSource"> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
971 <param name="geneSource" value="history" /> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
972 <param name="genomeFastaFiles" value="tophat_test.fa" /> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
973 <param name="genomeSAindexNbases" value="10" /> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
974 </conditional> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
975 <section name="oformat"> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
976 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
977 </section> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
978 <section name="algo"> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
979 <conditional name="params"> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
980 <param name="settingsType" value="default" /> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
981 </conditional> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
982 </section> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
983 <output name="output_log" file="rnastar_test_genomeSAindexNbases_02.log" compare="re_match_multiline" /> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
984 <output name="splice_junctions" file="rnastar_test_genomeSAindexNbases_02.bed"/> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
985 <output name="mapped_reads" file="rnastar_test_mapped_reads_genomeSAindexNbases_02.bam" compare="sim_size" delta="634" /> |
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
986 </test> |
23
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
987 <!-- test paired-end input and outWig --> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
988 <test expect_num_outputs="6"> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
989 <conditional name="singlePaired"> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
990 <param name="sPaired" value="paired" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
991 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
992 <param name="input2" value="tophat_in3.fastqsanger" ftype="fastqsanger" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
993 </conditional> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
994 <conditional name="refGenomeSource"> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
995 <param name="geneSource" value="history" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
996 <param name="genomeFastaFiles" value="tophat_test.fa" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
997 <param name="genomeSAindexNbases" value="5" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
998 <conditional name="GTFconditional"> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
999 <param name="GTFselect" value="with-gtf" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1000 <param name="sjdbOverhang" value="75"/> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1001 <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1002 <conditional name="quantmode_output"> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1003 <param name="quantMode" value="GeneCounts"/> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1004 </conditional> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1005 </conditional> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1006 </conditional> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1007 <section name="oformat"> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1008 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1009 </section> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1010 <section name="algo"> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1011 <conditional name="params"> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1012 <param name="settingsType" value="default" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1013 </conditional> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1014 </section> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1015 <conditional name="outWig"> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1016 <param name="outWigType" value="wiggle" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1017 <param name="outWigTypeSecondWord" value="read2"/> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1018 <param name="outWigStrand" value="false" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1019 </conditional> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1020 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1021 <output name="splice_junctions" file="rnastar_test_splicejunctions_PE.bed"/> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1022 <output name="mapped_reads" file="rnastar_test_mapped_reads_PE.bam" compare="sim_size" delta="634" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1023 <output name="reads_per_gene" file="tophat_test_reads_per_gene_PE.txt" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1024 <output name="signal_unique_str1" file="tophat_Signal.Unique.both.read2.out.wig" ftype="wig"/> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1025 <output name="signal_uniquemultiple_str1" file="tophat_Signal.Unique.both.read2.out.wig" ftype="wig" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1026 </test> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1027 <!-- test paired-end input as collection and outWig stranded --> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1028 <test expect_num_outputs="8"> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1029 <conditional name="singlePaired"> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1030 <param name="sPaired" value="paired_collection" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1031 <param name="input" > |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1032 <collection type="paired"> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1033 <element name="forward" value="tophat_revlib_R1.fastqsanger" ftype="fastq"/> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1034 <element name="reverse" value="tophat_revlib_R2.fastqsanger" ftype="fastq"/> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1035 </collection> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1036 </param> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1037 </conditional> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1038 <conditional name="refGenomeSource"> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1039 <param name="geneSource" value="history" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1040 <param name="genomeFastaFiles" value="tophat_test.fa" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1041 <param name="genomeSAindexNbases" value="5" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1042 <conditional name="GTFconditional"> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1043 <param name="GTFselect" value="with-gtf" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1044 <param name="sjdbOverhang" value="75"/> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1045 <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1046 <conditional name="quantmode_output"> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1047 <param name="quantMode" value="GeneCounts"/> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1048 </conditional> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1049 </conditional> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1050 </conditional> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1051 <section name="oformat"> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1052 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1053 </section> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1054 <section name="algo"> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1055 <conditional name="params"> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1056 <param name="settingsType" value="default" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1057 </conditional> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1058 </section> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1059 <conditional name="outWig"> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1060 <param name="outWigType" value="bedGraph" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1061 </conditional> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1062 |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1063 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1064 <output name="splice_junctions"> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1065 <assert_contents> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1066 <has_n_lines n="2"/> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1067 <has_line_matching expression="test_chromosome\s+251\s+350\s+1\s+1\s+0\s+24\s+0\s+33"/> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1068 <has_line_matching expression="test_chromosome\s+401\s+500\s+1\s+1\s+0\s+25\s+0\s+36"/> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1069 </assert_contents> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1070 </output> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1071 <output name="mapped_reads" > |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1072 <assert_contents> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1073 <has_size value="4711" delta="800"/> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1074 </assert_contents> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1075 </output> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1076 <output name="reads_per_gene" file="tophat_test_reads_per_gene_PE_rev.txt" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1077 <output name="signal_unique_str1" file="tophat_rev_Signal.Unique.str1.out.bg" ftype="bedgraph"/> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1078 <output name="signal_uniquemultiple_str1" file="tophat_rev_Signal.Unique.str1.out.bg" ftype="bedgraph"/> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1079 <output name="signal_unique_str2" file="tophat_rev_Signal.Unique.str2.out.bg" ftype="bedgraph" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1080 <output name="signal_uniquemultiple_str2" file="tophat_rev_Signal.Unique.str2.out.bg" ftype="bedgraph" /> |
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
22
diff
changeset
|
1081 </test> |
18
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
iuc
parents:
16
diff
changeset
|
1082 </tests> |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
1083 <help><![CDATA[ |
2
ace9f5a2b40f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents:
1
diff
changeset
|
1084 **What it does** |
ace9f5a2b40f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents:
1
diff
changeset
|
1085 |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
1086 STAR_ is an ultrafast universal RNA-seq aligner. |
0
b2326241bb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff
changeset
|
1087 |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
1088 **Compatibility Notes** |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
1089 |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
1090 STAR has a huge amount of options to filter alignments and to configure the |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
1091 exact format of its output. |
2
ace9f5a2b40f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3
iuc
parents:
1
diff
changeset
|
1092 |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
1093 Some tools you may plan to use in your downstream analysis of the results are known to be sensitive to these settings or combinations of them. |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
1094 |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
1095 *STAR-Fusion* |
0
b2326241bb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff
changeset
|
1096 |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
1097 STAR-Fusion_ can use the chimeric junctions output of STAR as input, but you |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
1098 need to enable **chimeric alignment detection** by STAR for that dataset to be |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
1099 generated. Hence, be sure to select: |
0
b2326241bb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff
changeset
|
1100 |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
1101 **Report chimeric alignments?**: `As separate tabular "Junctions" output (Junctions)`. |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
1102 |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
1103 In addition, for best results it is recommended_ that you |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
1104 |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
1105 - use **2-pass mapping** for more sensitive novel splice junction discovery |
0
b2326241bb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff
changeset
|
1106 |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
1107 - under *BAM output format specification*, |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
1108 **Read alignment tags to include in the BAM output**: select `XS` as an |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
1109 additional tag to generate (this is the equivalent of using |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
1110 `--outSAMstrandField intronMotif` on the command line) |
0
b2326241bb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff
changeset
|
1111 |
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
1112 - under *Algorithmic settings*, **Configure seed, alignment and limits options**: |
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
9
diff
changeset
|
1113 `use parameters suggested for STAR-Fusion`. |
0
b2326241bb09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 13522d2ad2efbb8dab405723f491bd1a6591e3ef
iuc
parents:
diff
changeset
|
1114 |
22
980d2a2e1180
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
parents:
20
diff
changeset
|
1115 *Arriba* |
980d2a2e1180
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
parents:
20
diff
changeset
|
1116 |
980d2a2e1180
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
iuc
parents:
20
diff
changeset
|
1117 Arriba_ can use the BAM with chimeric junctions or both files separately, generated by STAR, as input, but you |
980d2a2e1180
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1118 need to enable **chimeric alignment detection** by STAR for those datasets to be |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
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1119 generated. Hence, be sure to select either: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
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1120 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
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1121 **Report chimeric alignments?**: `As separate tabular "Junctions" output (Junctions)` or **Report chimeric alignments?**: `Within the BAM output (together with regular alignments; WithinBAM)`. |
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1122 |
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1123 In addition, the following parameters_ related to chimeric alignment are recommended for improved sensitivity |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
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1124 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
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1125 - under *Output filter criteria*, |
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1126 **Would you like to set additional output filters?**: select `Yes` to set |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
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1127 **Maximum number of alignments to output a read's alignment results, plus 1** to 50 |
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1128 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
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1129 - under *Algorithmic settings*, **Configure seed, alignment and limits options**: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 798abf3172360e7e09d2036b04ee2090d28123bb
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1130 `use parameters suggested for Arriba`. |
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1131 |
10
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1132 *Cufflinks* |
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1133 |
10
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1134 .. class:: infomark |
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1135 |
10
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1136 Cufflinks is not considered to be the best tool for use downstream of STAR |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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1137 anymore. Consider using *Stringtie* instead, which also should pose no |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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1138 compatibility issues. |
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1139 |
10
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1140 To avoid compatibility issues with Cufflinks you should: |
0
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1141 |
10
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1142 - select **XS** as a *Read alignment tag to include in the BAM output* if (and |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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1143 only if) your sequenced reads come from an unstranded library prep |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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1144 - *not* select the *jM* and *jI* tags for inclusion |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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1145 - keep the **HI** tag selected and |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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1146 - select *HI tag values should be* **zero-based** |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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1147 - exclude **All alignments across non-canonical junctions** under *Output |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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1148 filter criteria -> Exclude the following records from the BAM output* |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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1149 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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1150 ----- |
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1151 |
10
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1152 Attribution |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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1153 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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1154 Minor tweaks to output names to suit downstream purposes, toolshed automated |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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1155 dependencies and odds and ends of other code and documentation comprising |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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1156 this tool were originally written by Ross Lazarus and have been licensed under |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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1157 the creative commons |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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1158 `BY-NC_ND 3.0 license <http://creativecommons.org/licenses/by-nc-nd/3.0/>`__. |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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1159 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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1160 .. _STAR: https://github.com/alexdobin/STAR |
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1161 .. _STAR-Fusion: https://github.com/STAR-Fusion/STAR-Fusion |
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1162 .. _Arriba: https://github.com/suhrig/arriba |
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1163 .. _recommended: https://github.com/STAR-Fusion/STAR-Fusion/wiki#alternatively-kickstart-mode-running-star-yourself-and-then-running-star-fusion-using-the-existing-outputs |
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1164 .. _parameters: https://arriba.readthedocs.io/en/latest/workflow/ |
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1165 ]]></help> |
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1166 <expand macro="citations"/> |
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1167 </tool> |