Mercurial > repos > iuc > rgrnastar
annotate macros.xml @ 30:4014de1b6daf draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151
| author | iuc |
|---|---|
| date | Tue, 27 Aug 2024 14:11:16 +0000 |
| parents | b0f2be869d6d |
| children |
| rev | line source |
|---|---|
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3
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
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1 <macros> |
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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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2 <!-- REMEMBER to bump the version of @IDX_VERSION_SUFFIX@ |
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a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
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3 whenever you make changes to the @TOOL_VERSION@ token! |
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b9e04854e2bb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
iuc
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4 The data manager uses a symlink to this macro file to keep the STAR and |
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a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
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diff
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5 the index versions in sync, but you should manually update @IDX_VERSION_SUFFIX@ --> |
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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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6 <!-- STAR version to be used --> |
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3e94726bfa9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
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7 <token name="@TOOL_VERSION@">2.7.11a</token> |
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30
4014de1b6daf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151
iuc
parents:
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8 <token name="@VERSION_SUFFIX@">1</token> |
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a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
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9 <token name="@PROFILE@">21.01</token> |
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10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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10 <!-- STAR index version compatible with this version of STAR |
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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 This is the STAR version that introduced the index structure expected |
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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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12 by the current version. |
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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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13 It can be found for any specific version of STAR with: |
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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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14 STAR -h | grep versionGenome |
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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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15 or by looking for the versionGenome parameter in source/parametersDefault |
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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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16 of STAR's source code --> |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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17 <token name="@IDX_VERSION@">2.7.4a</token> |
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b0f2be869d6d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit adf08f34d44da2ba5b3010a7ae3e4a7702e9b9b1
iuc
parents:
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18 <token name="@IDX_VERSION_SUFFIX@">2</token> |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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19 <token name="@IDX_DATA_TABLE@">rnastar_index2x_versioned</token> |
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3
318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
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20 <xml name="requirements"> |
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318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
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21 <requirements> |
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a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
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22 <requirement type="package" version="@TOOL_VERSION@">star</requirement> |
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3e94726bfa9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
parents:
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23 <requirement type="package" version="1.18">samtools</requirement> |
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3e94726bfa9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
parents:
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24 <requirement type="package" version="1.13">gzip</requirement> |
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30
4014de1b6daf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151
iuc
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25 <yield/> |
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318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
iuc
parents:
diff
changeset
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26 </requirements> |
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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 </xml> |
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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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28 <xml name="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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29 <edam_topics> |
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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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30 <edam_topic>topic_3170</edam_topic> |
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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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31 <edam_topic>topic_3308</edam_topic> |
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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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32 </edam_topics> |
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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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33 <edam_operations> |
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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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34 <edam_operation>operation_0292</edam_operation> |
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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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35 </edam_operations> |
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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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36 </xml> |
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41929aa1e7f3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2911002ccd79fe062f6346ee5699ea262f92f04f"
iuc
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37 <xml name="index_selection" token_with_gene_model="0"> |
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30
4014de1b6daf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151
iuc
parents:
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38 <param argument="--genomeDir" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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39 <options from_data_table="@IDX_DATA_TABLE@"> |
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30
4014de1b6daf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151
iuc
parents:
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40 <filter type="static_value" column="4" value="@WITH_GENE_MODEL@"/> |
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4014de1b6daf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151
iuc
parents:
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41 <filter type="static_value" column="5" value="@IDX_VERSION@"/> |
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4014de1b6daf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151
iuc
parents:
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42 <filter type="sort_by" column="2"/> |
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4014de1b6daf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151
iuc
parents:
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43 <validator type="no_options" message="No indexes are available for the selected input dataset"/> |
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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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44 </options> |
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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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45 </param> |
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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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46 </xml> |
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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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47 <token name="@FASTQ_GZ_OPTION@"> |
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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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48 --readFilesCommand zcat |
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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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49 </token> |
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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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50 <xml name="citations"> |
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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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51 <citations> |
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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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52 <citation type="doi">10.1093/bioinformatics/bts635</citation> |
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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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53 </citations> |
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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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54 </xml> |
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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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55 <xml name="SJDBOPTIONS"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151
iuc
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56 <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="false" help="Exon junction information for mapping splices"/> |
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4014de1b6daf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151
iuc
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57 <param argument="--sjdbGTFfeatureExon" type="text" value="exon" label="Elements to use from the gene model to use for splice junctions" help="By default and for almost all cases: 'exon', referring to finding junctions at the RNA splice sites. This can optionally be changed to allow splicing at other levels, such as 'gene', 'transcript', 'CDS'."/> |
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4014de1b6daf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151
iuc
parents:
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58 <param argument="--sjdbOverhang" type="integer" min="1" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1"/> |
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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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59 </xml> |
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8
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167
iuc
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60 <xml name="dbKeyActions"> |
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d5659efd66aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167
iuc
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61 <actions> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
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62 <expand macro="dbKeyAction"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167
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63 </actions> |
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d5659efd66aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit be695260aa6fe507c80f932ea9b2e63b2662d167
iuc
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64 </xml> |
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24
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
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65 <xml name="dbKeyAction"> |
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4df95e2d7f61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
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66 <conditional name="refGenomeSource.geneSource"> |
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4df95e2d7f61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
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67 <when value="indexed"> |
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4df95e2d7f61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
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68 <action type="metadata" name="dbkey"> |
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4df95e2d7f61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
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69 <option type="from_data_table" name="@IDX_DATA_TABLE@" column="1" offset="0"> |
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4df95e2d7f61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
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70 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> |
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4df95e2d7f61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents:
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71 <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/> |
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4df95e2d7f61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
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72 </option> |
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4df95e2d7f61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
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changeset
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73 </action> |
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4df95e2d7f61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents:
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|
74 </when> |
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4df95e2d7f61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents:
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changeset
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75 <when value="history"> |
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4df95e2d7f61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents:
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76 <action type="metadata" name="dbkey"> |
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30
4014de1b6daf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151
iuc
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77 <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey"/> |
|
24
4df95e2d7f61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents:
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78 </action> |
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4df95e2d7f61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents:
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changeset
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79 </when> |
|
4df95e2d7f61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents:
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changeset
|
80 </conditional> |
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4df95e2d7f61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
iuc
parents:
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81 </xml> |
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10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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82 <token name="@TEMPINDEX@"><![CDATA[ |
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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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83 ## Create temporary index for custom reference |
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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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changeset
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84 #if str($refGenomeSource.geneSource) == 'history': |
|
23
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
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85 #if $refGenomeSource.genomeFastaFiles.ext == "fasta" |
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a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
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86 ln -s '$refGenomeSource.genomeFastaFiles' refgenome.fa && |
|
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
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87 #else |
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a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
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88 gunzip -c '$refGenomeSource.genomeFastaFiles' > refgenome.fa && |
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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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89 #end if |
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10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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90 mkdir -p tempstargenomedir && |
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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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91 STAR |
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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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92 --runMode genomeGenerate |
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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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93 --genomeDir 'tempstargenomedir' |
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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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94 --genomeFastaFiles refgenome.fa |
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10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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95 ## Handle difference between indices with/without annotations |
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15
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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96 #if 'GTFconditional' in $refGenomeSource: |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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97 ## GTFconditional exists only in STAR, but not STARsolo |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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98 #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf': |
|
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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99 --sjdbOverhang '${refGenomeSource.GTFconditional.sjdbOverhang}' |
|
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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diff
changeset
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100 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}' |
|
27
79de45b5069b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
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101 --sjdbGTFfeatureExon '${refGenomeSource.GTFconditional.sjdbGTFfeatureExon}' |
|
15
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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102 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3': |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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103 --sjdbGTFtagExonParentTranscript Parent |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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104 #end if |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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105 #end if |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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106 #else: |
|
27
79de45b5069b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
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107 ## ref genome selection is less complex for STARsolo because |
|
15
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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108 ## with-gtf is mandatory there |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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109 --sjdbOverhang '${refGenomeSource.sjdbOverhang}' |
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5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents:
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110 --sjdbGTFfile '${refGenomeSource.sjdbGTFfile}' |
|
27
79de45b5069b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents:
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111 --sjdbGTFfeatureExon '${refGenomeSource.sjdbGTFfeatureExon}' |
|
15
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
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112 #if str($refGenomeSource.sjdbGTFfile.ext) == 'gff3': |
|
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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113 --sjdbGTFtagExonParentTranscript Parent |
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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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114 #end if |
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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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115 #end if |
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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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116 #if str($refGenomeSource.genomeSAindexNbases): |
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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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117 --genomeSAindexNbases ${refGenomeSource.genomeSAindexNbases} |
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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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118 #end if |
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28
3e94726bfa9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
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119 ## Diploid mode |
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3e94726bfa9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
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120 #if 'diploidconditional' in $refGenomeSource: |
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3e94726bfa9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
parents:
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121 #if str($refGenomeSource.diploidconditional.diploid) == 'Yes': |
|
3e94726bfa9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
parents:
27
diff
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122 --genomeTransformVCF '${refGenomeSource.diploidconditional.genomeTransformVCF}' |
|
3e94726bfa9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
parents:
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diff
changeset
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123 --genomeTransformType Diploid |
|
3e94726bfa9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
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124 #end if |
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3e94726bfa9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 452556bcdcc3fe4e9ace07201be2365cd6f99e2f
iuc
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125 #end if |
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10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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126 --runThreadN \${GALAXY_SLOTS:-4} |
|
23
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
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127 ## in bytes |
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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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128 --limitGenomeGenerateRAM \$((\${GALAXY_MEMORY_MB:-31000} * 1000000)) |
|
10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
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129 && |
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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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130 #end if |
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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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131 ]]></token> |
|
30
4014de1b6daf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151
iuc
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132 <token name="@REFGENOMEHANDLING@"><![CDATA[ |
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10
d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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133 --runThreadN \${GALAXY_SLOTS:-4} |
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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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134 --genomeLoad NoSharedMemory |
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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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135 --genomeDir |
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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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136 #if str($refGenomeSource.geneSource) == 'history': |
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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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137 tempstargenomedir |
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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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138 #else: |
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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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|
139 '${refGenomeSource.GTFconditional.genomeDir.fields.path}' |
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d82339e37e8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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140 ## Handle difference between indices with/without annotations |
|
23
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
18
diff
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141 #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf-with-gtf': |
|
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
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142 --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang |
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a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
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diff
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143 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}' |
|
27
79de45b5069b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
iuc
parents:
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144 --sjdbGTFfeatureExon '${refGenomeSource.GTFconditional.sjdbGTFfeatureExon}' |
|
23
a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
iuc
parents:
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145 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3': |
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a2b0feda6933
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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146 --sjdbGTFtagExonParentTranscript Parent |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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147 #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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148 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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149 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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150 ]]></token> |
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151 <token name="@READSHANDLING@"><![CDATA[ |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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152 ## Check that the input pairs are of the same type |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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153 ## otherwise STARsolo will run for a long time and then error out. |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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154 ## We consume either repeats of two inputs R1 + R2 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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155 ## or a collection of paired reads. |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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156 #if str($sc.input_types.use) == "repeat": |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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157 #set $reads1 = [] |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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158 #set $reads2 = [] |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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159 #for $r1, $r2 in zip($sc.input_types.input1, $sc.input_types.input2): |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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160 #assert $r1.datatype == $r2.datatype |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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161 #silent $reads1.append(str($r1)) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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162 #silent $reads2.append(str($r2)) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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163 #end for |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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164 #set $reads1 = ','.join($reads1) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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165 #set $reads2 = ','.join($reads2) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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166 #elif str($sc.input_types.use) == "list_paired": |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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167 #set $r1 = $sc.input_types.input_collection.forward |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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168 #set $r2 = $sc.input_types.input_collection.reverse |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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169 #set $reads1 = $r1 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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170 #set $reads2 = $r2 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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171 #end if |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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172 ## cDNA sequence(s) [R2] always go first, then barcode(s) [R1] |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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173 ## see: Section 3.2 of STAR manual for multiple inputs, and Section 13 for STARsolo inputs |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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174 --readFilesIn $reads2 $reads1 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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175 --soloCBmatchWLtype $sc.soloCBmatchWLtype |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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176 #if $r1.is_of_type('fastq.gz', 'fastqsanger.gz'): |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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177 @FASTQ_GZ_OPTION@ |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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178 #end if |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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179 ]]></token> |
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30
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180 <token name="@LIMITS@"><![CDATA[ |
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181 --limitOutSJoneRead $getVar('algo.params.junction_limits.limitOutSJoneRead', $getVar('solo.junction_limits.limitOutSJoneRead', 1000)) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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182 --limitOutSJcollapsed $getVar('algo.params.junction_limits.limitOutSJcollapsed', $getVar('solo.junction_limits.limitOutSJcollapsed', 1000000)) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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183 --limitSjdbInsertNsj $getVar('algo.params.junction_limits.limitSjdbInsertNsj', $getVar('solo.junction_limits.limitSjdbInsertNsj', 1000000)) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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184 ]]></token> |
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15
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
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185 <xml name="ref_selection"> |
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30
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151
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186 <param argument="--genomeFastaFiles" type="data" format="fasta,fasta.gz" label="Select a reference genome"/> |
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187 <param argument="--genomeSAindexNbases" type="integer" min="2" max="16" value="14" label="Length of the SA pre-indexing string" help="Typically between 10 and 15. Longer strings will use much more memory, but allow faster searches. For small genomes, the parameter --genomeSAindexNbases must be scaled down to min(14, log2(GenomeLength)/2 - 1)"/> |
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15
5ec75f5dae3c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
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188 </xml> |
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189 <xml name="stdio"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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190 <stdio> |
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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 <regex match="FATAL error" source="both" level="fatal"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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192 <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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193 <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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194 <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/> |
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195 <yield/> |
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196 </stdio> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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197 </xml> |
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17
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198 <xml name="input_selection"> |
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199 <conditional name="input_types"> |
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200 <param name="use" type="select" label="Input Type"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151
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201 <option value="repeat">Separate barcode and cDNA reads</option> |
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202 <option value="list_paired">Paired collection of barcode and cDNA reads</option> |
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17
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203 </param> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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204 <when value="repeat"> |
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205 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" multiple="true" label="RNA-Seq FASTQ/FASTA file, Barcode reads"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151
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206 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input2" type="data" multiple="true" label="RNA-Seq FASTQ/FASTA file, cDNA reads"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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207 </when> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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208 <when value="list_paired"> |
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209 <param name="input_collection" collection_type="paired" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="Collection of Pairs"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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210 </when> |
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211 </conditional> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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212 </xml> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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213 <xml name="input_selection_smart_seq"> |
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214 <conditional name="input_types_smart_seq"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151
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215 <param name="use" type="select" label="Input Type"> |
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216 <option value="list_single_end">Single-end FASTQ collection</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151
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217 <option value="list_paired_end">Paired FASTQ collection</option> |
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17
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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218 </param> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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219 <when value="list_single_end"> |
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220 <param name="single_end_collection" collection_type="list" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="List of single-end FASTQ files"/> |
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17
7ed2edc1337f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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221 </when> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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222 <when value="list_paired_end"> |
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223 <param name="paired_end_collection" collection_type="list:paired" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="List of paired-end FASTQ files"/> |
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17
7ed2edc1337f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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224 </when> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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225 </conditional> |
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7ed2edc1337f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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226 </xml> |
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7ed2edc1337f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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227 <xml name="umidedup_options"> |
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228 <option value="1MM_All" selected="true">Collapse all UMIs with 1 mismatch distance to each other (1MM_All)</option> |
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229 <option value="1MM_Directional_UMItools">Directional method from the UMI-tool</option> |
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230 <option value="1MM_Directional">Directional with stringent UMI deduplication</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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231 </xml> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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232 <xml name="anchor_types"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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233 <option value="0">Read start</option> |
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7ed2edc1337f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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234 <option value="1">Read end</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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235 <option value="2">Adapter start</option> |
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7ed2edc1337f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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236 <option value="3">Adapter end</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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237 </xml> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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238 <xml name="cb_match_wl_common"> |
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239 <option value="Exact">Exact</option> |
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240 <option value="1MM">Single match (1MM)</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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241 </xml> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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242 <xml name="cb_match_wl_cellranger"> |
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30
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243 <option value="1MM_multi" selected="true">Multiple matches (CellRanger 2, 1MM_multi)</option> |
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244 <option value="1MM_multi_pseudocounts">Multiple matches (CellRanger 3, 1MM_multi_pseudocounts)</option> |
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245 <option value="1MM_multi_Nbase_pseudocounts">Multimatching to WL is allowed for CBs with N-bases (CellRanger 3, 1MM_multi_Nbase_pseudocounts)</option> |
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c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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246 </xml> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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247 <xml name="solo_adapter_params"> |
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248 <param argument="--soloAdapterSequence" type="text" value="-" label="Adapter sequence to anchor barcodes."> |
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18
c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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249 <sanitizer> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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250 <valid initial="string.digits"> |
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c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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251 <add value="-"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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252 <add value="A"/> |
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c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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253 <add value="T"/> |
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c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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254 <add value="C"/> |
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c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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255 <add value="G"/> |
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c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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256 <add value="N"/> |
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c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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257 </valid> |
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c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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258 </sanitizer> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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259 </param> |
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260 <param argument="--soloAdapterMismatchesNmax" type="integer" min="1" value="1" label="Maximum number of mismatches allowed in adapter sequence"/> |
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261 <param argument="--clipAdapterType" type="select"> |
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262 <option value="Hamming" selected="true">Adapter clipping based on Hamming distance</option> |
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263 <option value="CellRanger4">5p and 3p adapter clipping similar to CellRanger4</option> |
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264 <option value="None">No adapter clipping</option> |
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c772497b2c32
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit d0c9fa48df667ffad1abd71164e6bb1d9cb16bd9"
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265 </param> |
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17
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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266 </xml> |
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267 <xml name="common_SAM_attributes"> |
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268 <option value="NH" selected="true">NH (number of reported alignments/hits for the read)</option> |
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269 <option value="HI" selected="true">HI (query hit index)</option> |
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270 <option value="AS" selected="true">AS (local alignment score)</option> |
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271 <option value="nM" selected="true">nM (number of mismatches per (paired) alignment)</option> |
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272 <option value="NM">NM (edit distance of the aligned read to the reference)</option> |
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273 <option value="MD">MD (string for mismatching positions)</option> |
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274 <option value="jM">jM (intron motifs for all junctions)</option> |
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275 <option value="jI">jI (1-based start and end of introns for all junctions)</option> |
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276 </xml> |
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277 <xml name="limits"> |
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278 <section name="junction_limits" title="Junction Limits" expanded="false"> |
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279 <param argument="--limitOutSJoneRead" type="integer" min="1" value="1000" label="Maximum number of junctions for one read (including all multimappers)"/> |
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280 <param argument="--limitOutSJcollapsed" type="integer" min="1" value="1000000" label="Maximum number of collapsed junctions"/> |
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281 <param argument="--limitSjdbInsertNsj" type="integer" min="0" value="1000000" label="Maximum number of inserts to be inserted into the genome on the fly."/> |
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282 </section> |
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283 </xml> |
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284 <xml name="outCountActions"> |
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285 <actions> |
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286 <action name="column_names" type="metadata" default="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand"/> |
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287 <expand macro="dbKeyAction"/> |
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288 </actions> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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289 </xml> |
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290 <xml name="outWig"> |
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291 <conditional name="outWig"> |
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292 <param name="outWigType" type="select" label="Compute coverage"> |
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293 <option value="None">No coverage</option> |
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294 <option value="bedGraph">Yes in bedgraph format</option> |
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295 <option value="wiggle">Yes in wiggle format</option> |
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296 </param> |
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297 <when value="None"> |
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298 <!-- This is necessary for the filtering of output --> |
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299 <param name="outWigStrand" type="hidden" value="false"/> |
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300 </when> |
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301 <when value="bedGraph"> |
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302 <expand macro="outWigParams"/> |
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303 </when> |
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304 <when value="wiggle"> |
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305 <expand macro="outWigParams"/> |
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306 </when> |
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307 </conditional> |
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308 </xml> |
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309 <xml name="outWigParams"> |
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310 <param name="outWigTypeSecondWord" type="select" label="Input for coverage"> |
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311 <option value="">Default (everything that mapped)</option> |
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312 <option value="read_5p">signal from only 5’ of the 1st read</option> |
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313 <option value="read2">signal from only 2nd read</option> |
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314 </param> |
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26
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315 <param argument="--outWigStrand" type="boolean" truevalue="Stranded" falsevalue="Unstranded" checked="true" label="Generate a coverage for each strand (stranded coverage)"/> |
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316 <param argument="--outWigReferencesPrefix" type="text" value="-" label="prefix matching reference name" help="For example, set 'chr' if you mapped on an ensembl genome but you want to display on UCSC"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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317 <param argument="--outWigNorm" type="boolean" truevalue="RPM" falsevalue="None" checked="true" label="Normalize coverage to million of mapped reads (RPM)"/> |
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318 </xml> |
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319 <token name="@OUTWIG@"><![CDATA[ |
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320 #if str($outWig.outWigType) != 'None': |
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321 --outWigType '$outWig.outWigType' '$outWig.outWigTypeSecondWord' |
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322 --outWigStrand '$outWig.outWigStrand' |
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323 --outWigReferencesPrefix '$outWig.outWigReferencesPrefix' |
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324 --outWigNorm '$outWig.outWigNorm' |
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325 #end if |
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326 ]]></token> |
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327 <token name="@OUTWIGOUTPUTS@"><![CDATA[ |
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328 #if str($outWig.outWigType) == "bedGraph": |
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329 && mv Signal.Unique.str1.out.bg Signal.Unique.str1.out |
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330 && mv Signal.UniqueMultiple.str1.out.bg Signal.UniqueMultiple.str1.out |
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331 #if str($outWig.outWigStrand) == "Stranded": |
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332 && mv Signal.Unique.str2.out.bg Signal.Unique.str2.out |
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333 && mv Signal.UniqueMultiple.str2.out.bg Signal.UniqueMultiple.str2.out |
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334 #end if |
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335 #elif str($outWig.outWigType) == "wiggle": |
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336 && mv Signal.Unique.str1.out.wig Signal.Unique.str1.out |
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337 && mv Signal.UniqueMultiple.str1.out.wig Signal.UniqueMultiple.str1.out |
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338 #if str($outWig.outWigStrand) == "Stranded": |
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339 && mv Signal.Unique.str2.out.wig Signal.Unique.str2.out |
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340 && mv Signal.UniqueMultiple.str2.out.wig Signal.UniqueMultiple.str2.out |
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341 #end if |
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342 #end if |
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343 ]]></token> |
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344 <xml name="outWigOutputs"> |
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345 <data format="bedgraph" name="signal_unique_str1" label="${tool.name} on ${on_string}: Coverage Uniquely mapped strand 1" from_work_dir="Signal.Unique.str1.out"> |
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346 <filter>outWig['outWigType'] != "None"</filter> |
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347 <expand macro="dbKeyActions"/> |
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348 <change_format> |
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349 <when input="outWig.outWigType" value="wiggle" format="wig"/> |
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350 </change_format> |
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351 </data> |
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352 <data format="bedgraph" name="signal_uniquemultiple_str1" label="${tool.name} on ${on_string}: Coverage Uniquely + Multiple mapped strand 1" from_work_dir="Signal.UniqueMultiple.str1.out"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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353 <filter>outWig['outWigType'] != "None"</filter> |
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354 <expand macro="dbKeyActions"/> |
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355 <change_format> |
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356 <when input="outWig.outWigType" value="wiggle" format="wig"/> |
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357 </change_format> |
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358 </data> |
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359 <data format="bedgraph" name="signal_unique_str2" label="${tool.name} on ${on_string}: Coverage Uniquely mapped strand 2" from_work_dir="Signal.Unique.str2.out"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
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360 <filter>outWig['outWigType'] != "None" and outWig['outWigStrand']</filter> |
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30
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361 <expand macro="dbKeyActions"/> |
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362 <change_format> |
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363 <when input="outWig.outWigType" value="wiggle" format="wig"/> |
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364 </change_format> |
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365 </data> |
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366 <data format="bedgraph" name="signal_uniquemultiple_str2" label="${tool.name} on ${on_string}: Coverage Uniquely + Multiple mapped strand 2" from_work_dir="Signal.UniqueMultiple.str2.out"> |
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367 <filter>outWig['outWigType'] != "None" and outWig['outWigStrand']</filter> |
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368 <expand macro="dbKeyActions"/> |
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369 <change_format> |
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370 <when input="outWig.outWigType" value="wiggle" format="wig"/> |
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371 </change_format> |
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372 </data> |
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373 </xml> |
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374 <xml name="quantMode"> |
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375 <conditional name="quantmode_output"> |
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376 <param argument="--quantMode" type="select" label="Per gene/transcript output" help="STAR can provide analysis results not only with respect to the reference genome, but also with respect to genes and transcripts described by a gene model. Note: This functionality requires either the selection above of a cached index with a gene model, or a gene model provided alongside the index/reference genome in GTF or GFF3 format!"> |
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377 <option value="-">No per gene or transcript output</option> |
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378 <option value="GeneCounts">Per gene read counts (GeneCounts)</option> |
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379 <option value="TranscriptomeSAM">Transcript-based BAM output (TranscriptomeSAM)</option> |
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380 <option value="TranscriptomeSAM GeneCounts">Both per gene read counts and transcript-based BAM output (TranscriptomeSAM GeneCounts)</option> |
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381 </param> |
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382 <when value="-"/> |
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383 <when value="GeneCounts"/> |
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384 <when value="TranscriptomeSAM"> |
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385 <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend" label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?" help="You will need to exclude alignments with indels and soft-clipped bases from the transcriptome BAM output for compatibility with certain transcript quantification tools, most notably RSEM. If you are using a tool, like eXpress, that can deal with indels and soft-clipped bases, you can achieve better results by leaving this option disabled."/> |
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386 </when> |
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387 <when value="TranscriptomeSAM GeneCounts"> |
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388 <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend" label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?" help="You will need to exclude alignments with indels and soft-clipped bases from the transcriptome BAM output for compatibility with certain transcript quantification tools, most notably RSEM. If you are using a tool, like eXpress, that can deal with indels and soft-clipped bases, you can achieve better results by leaving this option disabled."/> |
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389 </when> |
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390 </conditional> |
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391 </xml> |
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392 <xml name="quantModeNoGTF"> |
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393 <conditional name="quantmode_output"> |
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394 <param argument="--quantMode" type="select" label="Per gene/transcript output"> |
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395 <option value="-">No per gene or transcript output as no GTF was provided</option> |
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396 </param> |
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397 <when value="-"/> |
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398 </conditional> |
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399 </xml> |
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400 <xml name="outSAMmapqUnique"> |
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401 <!-- MAPQ 255 is the default in STAR (coming from tophat behaviour and compatibility for Cufflinks) but it is a problematic value |
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402 - according to SAM/BAM specs it means "undefined". |
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403 - Using 255 as the max mapq causes problem with modern downstream tools like mutect2: https://sites.duke.edu/workblog/2021/08/18/star-rnaseq-gatk-mutect2/ and 60 has become an inofficial replacement for 255. --> |
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404 <param argument="--outSAMmapqUnique" type="integer" value="60" min="0" max="255" label="MAPQ value for unique mappers" help="STAR bases the mapping quality scores of alignment records in its BAM output on the number of alternative mappings for the read. If a read maps to multiple locations on the reference genome, the following MAPQ scoring scheme is used: >=5 mappings => MAPQ=0; 3-4 mappings => MAPQ=1; 2 mappings => MAPQ=3. This setting lets you control the MAPQ used for reads mapped to a single location. Set to 255 for compatibility with Cufflink (default in STAR) but keep to 60 for modern downstream tools like mutect2."/> |
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405 </xml> |
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406 <xml name="wasp"> |
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407 <!-- |
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408 This is re-implementation of the original WASP algorithm by Bryce van de Geijn, Graham McVicker, |
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409 Yoav Gilad and Jonathan K Pritchard. Please cite the original WASP paper: Nature Methods 12, |
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410 1061–1063 (2015) https://www.nature.com/articles/nmeth.3582. WASP filtering is activated |
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411 with "waspOutputMode SAMtag". |
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412 --> |
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413 <conditional name="wasp_conditional"> |
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414 <param argument="--waspOutputMode" type="select" label="Actiavte WASP filtering"> |
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415 <help><![CDATA[This is a reimplementation of the original WASP algorithm by Bryce van de Geijn, Graham McVicker, |
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416 Yoav Gilad and Jonathan K Pritchard. https://doi.org/10.1038/nmeth.3582. This option will add the vW tag to the SAM output. vW:i:1 means |
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417 alignment passed WASP filtering, and all other values mean it did not:<br/> |
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418 - vW:i:2 = multi-mapping read<br/> |
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419 - vW:i:3 = variant base in the read is N (non-ACGT)<br/> |
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420 - vW:i:4 = remapped read did not map <br/> |
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421 - vW:i:5 = remapped read multi-maps <br/> |
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422 - vW:i:6 = remapped read maps to a different locus <br/> |
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423 - vW:i:7 = read overlaps too many variants <br/> |
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424 ]]> |
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425 </help> |
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426 <option value="" selected="true">No WASP filtering</option> |
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427 <option value="wasp_mode">Activate WASP filtering</option> |
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428 </param> |
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429 <when value="wasp_mode"> |
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430 <param argument="--varVCFfile" type="data" format="vcf" label="VCF file with personal variants" help="Each variant is expected to have a genotype with two alleles. The VCF file needs to have the 10th column with genotype recorded as 0/1, 1/0, 1/1 (or | instead of /)"/> |
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4014de1b6daf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151
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431 </when> |
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4014de1b6daf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151
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432 <when value=""/> |
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4014de1b6daf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151
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433 </conditional> |
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4df95e2d7f61
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
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434 </xml> |
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318b2a9d54dd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 0d434bca5083e908114d93e11094e48f49b98ed1
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435 </macros> |