| Previous changeset 8:6b0ba6de1424 (2018-08-23) Next changeset 10:4de6e2e40c7a (2019-09-09) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4cc21e8c47d99cee4560bb7634c859b551c4ea72-dirty |
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modified:
salmon.xml tool_data_table_conf.xml.sample |
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added:
test-data/cached_locally/prebuilt_index/duplicate_clusters.tsv test-data/cached_locally/prebuilt_index/hash.bin test-data/cached_locally/prebuilt_index/header.json test-data/cached_locally/prebuilt_index/indexing.log test-data/cached_locally/prebuilt_index/quasi_index.log test-data/cached_locally/prebuilt_index/refInfo.json test-data/cached_locally/prebuilt_index/rsd.bin test-data/cached_locally/prebuilt_index/sa.bin test-data/cached_locally/prebuilt_index/txpInfo.bin test-data/cached_locally/prebuilt_index/versionInfo.json test-data/cached_locally/salmon_indexes_versioned.loc tool-data/salmon_indexes_versioned.loc.sample tool_data_table_conf.xml.test |
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removed:
tool-data/salmon_indexes.loc.sample |
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| diff -r 6b0ba6de1424 -r 2c0ca397d302 salmon.xml --- a/salmon.xml Thu Aug 23 15:58:26 2018 -0400 +++ b/salmon.xml Sat Jul 27 12:37:47 2019 -0400 |
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| @@ -18,6 +18,7 @@ </param> </xml> <token name="@VERSION@">0.11.2</token> + <token name="@IDX_VERSION@">q5</token> </macros> <requirements> @@ -230,8 +231,9 @@ </param> <when value="indexed"> <param name="index" type="select" label="Select a reference transcriptome" help="If your transcriptome of interest is not listed, contact your Galaxy admin"> - <options from_data_table="salmon_indexes"> + <options from_data_table="salmon_indexes_versioned"> <filter type="sort_by" column="2"/> + <filter type="static_value" column="4" value="@IDX_VERSION@" /> <validator type="no_options" message="No indexes are available for the selected input dataset"/> </options> </param> @@ -441,6 +443,28 @@ </assert_contents> </output> </test> + <test> <!--test use of built-in index--> + <param name="single_or_paired_opts" value="paired" /> + <param name="input_mate1" value="reads_1.fastq" /> + <param name="input_mate2" value="reads_2.fastq" /> + <param name="biasCorrect" value="False" /> + <param name="TranscriptSource" value="indexed" /> + <param name="index" value="hg19_transcript_subset" /> + <output name="output_quant"> + <assert_contents> + <has_text text="EffectiveLength" /> + <has_text text="TPM" /> + <has_text text="NM_001168316" /> + <has_text text="NM_174914" /> + <has_text text="NM_018953" /> + <has_text text="NR_003084" /> + <has_text text="NM_017410" /> + <has_text text="NM_153693" /> + <has_text text="NR_031764" /> + <has_n_columns n="5" /> + </assert_contents> + </output> + </test> <test> <!-- gzipped input --> <param name="single_or_paired_opts" value="paired" /> <param name="input_mate1" value="reads_1.fastq.gz" ftype="fastqsanger.gz" /> |
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| diff -r 6b0ba6de1424 -r 2c0ca397d302 test-data/cached_locally/prebuilt_index/duplicate_clusters.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/prebuilt_index/duplicate_clusters.tsv Sat Jul 27 12:37:47 2019 -0400 |
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| @@ -0,0 +1,1 @@ +RetainedTxp DuplicateTxp |
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| diff -r 6b0ba6de1424 -r 2c0ca397d302 test-data/cached_locally/prebuilt_index/hash.bin |
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| Binary file test-data/cached_locally/prebuilt_index/hash.bin has changed |
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| diff -r 6b0ba6de1424 -r 2c0ca397d302 test-data/cached_locally/prebuilt_index/header.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/prebuilt_index/header.json Sat Jul 27 12:37:47 2019 -0400 |
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| @@ -0,0 +1,14 @@ +{ + "value0": { + "IndexType": 1, + "IndexVersion": "q5", + "UsesKmers": true, + "KmerLen": 31, + "BigSA": false, + "PerfectHash": false, + "SeqHash": "238a71484cdcf251805629c612f7edd515eb1a23d9be2e2014b62fd5931eb4ac", + "NameHash": "2fc64c34c65a78d18fec933772e1aa454cfed52b2b48d43eb75d2933a22feb04", + "SeqHash512": "a45ea3d0c5f11c16a45b8b75f902f908996117d7486d72b3d19a8ae619b07b22f3ca0888f5ee6e9dbabf639ae51f7fc74b8eea8808435bbb2ec70b96162849aa", + "NameHash512": "6123f1c58bf2153fca204e97fa72a2d25460242f14b886e421316ff251cc57293e77c02d536122e97f46d2508c626e42a35a1798209766359904ddf49fb7bf33" + } +} \ No newline at end of file |
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| diff -r 6b0ba6de1424 -r 2c0ca397d302 test-data/cached_locally/prebuilt_index/indexing.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/prebuilt_index/indexing.log Sat Jul 27 12:37:47 2019 -0400 |
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| @@ -0,0 +1,2 @@ +[2019-07-25 13:45:20.599] [jLog] [info] building index +[2019-07-25 13:45:20.654] [jLog] [info] done building index |
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| diff -r 6b0ba6de1424 -r 2c0ca397d302 test-data/cached_locally/prebuilt_index/refInfo.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/prebuilt_index/refInfo.json Sat Jul 27 12:37:47 2019 -0400 |
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| @@ -0,0 +1,5 @@ +{ + "ReferenceFiles": [ + "tools/salmon/test-data/transcripts.fasta" + ] +} \ No newline at end of file |
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| diff -r 6b0ba6de1424 -r 2c0ca397d302 test-data/cached_locally/prebuilt_index/rsd.bin |
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| Binary file test-data/cached_locally/prebuilt_index/rsd.bin has changed |
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| diff -r 6b0ba6de1424 -r 2c0ca397d302 test-data/cached_locally/prebuilt_index/sa.bin |
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| Binary file test-data/cached_locally/prebuilt_index/sa.bin has changed |
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| diff -r 6b0ba6de1424 -r 2c0ca397d302 test-data/cached_locally/prebuilt_index/txpInfo.bin |
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| Binary file test-data/cached_locally/prebuilt_index/txpInfo.bin has changed |
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| diff -r 6b0ba6de1424 -r 2c0ca397d302 test-data/cached_locally/prebuilt_index/versionInfo.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/prebuilt_index/versionInfo.json Sat Jul 27 12:37:47 2019 -0400 |
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| @@ -0,0 +1,6 @@ +{ + "indexVersion": 2, + "hasAuxIndex": false, + "auxKmerLength": 31, + "indexType": 1 +} \ No newline at end of file |
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| diff -r 6b0ba6de1424 -r 2c0ca397d302 test-data/cached_locally/salmon_indexes_versioned.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/salmon_indexes_versioned.loc Sat Jul 27 12:37:47 2019 -0400 |
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| @@ -0,0 +1,33 @@ +# salmon_indexes_versioned.loc.sample +# This is a *.loc.sample file distributed with Galaxy that enables tools +# to use a directory of indexed data files. This one is for Salmon. +# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup +# First create these data files and save them in your own data directory structure. +# Then, create a salmon_indexes_versioned.loc.sample file to use those indexes with tools. +# Copy this file, save it with the same name (minus the .sample), +# follow the format examples, and store the result in this directory. +# The file should include an one line entry for each index set. +# The path points to the "basename" for the set, not a specific file. +# It has four text columns seperated by TABS. +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> <version> +# +# The <version> column can be retrieved from the header.json file in the index folder. e.g "IndexVersion": "q5" + + + +# So, for example, if you had sacCer3 indexes stored in: +# +# /depot/data2/galaxy/sacCer3/salmon_indexes/ +# +# then the salmon_indexes.loc entry could look like this: +# +#sacCer3 sacCer3 S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3) /depot/data2/galaxy/sacCer3/salmon_indexes/version_3/ q6 +# +#More examples: +# +#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/salmon_indexes/mm10/version_2 q4 +#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/salmon_indexes/dm3/version_1 q5 +# +# +hg19_transcript_subset hg19 Human (Homo sapiens): hg19 transcript test subset ${__HERE__}/prebuilt_index q5 |
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| diff -r 6b0ba6de1424 -r 2c0ca397d302 tool-data/salmon_indexes.loc.sample --- a/tool-data/salmon_indexes.loc.sample Thu Aug 23 15:58:26 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,14 +0,0 @@ -# This is a sample file distributed with Galaxy that is used to define a -# list of salmon indices, using three columns tab separated: -# -# salmon_index_id{tab}Salmon Index desciption{tab}/data/salmon_indexes/salmon_index_id/ -# -# An index can be created with the following command: -# -# salmon index -# --transcripts your_transcripts.fasta -# --kmerSize 21 -# --out /data/salmon_indexes/salmon_index_id/ -# --threads 4 -# - |
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| diff -r 6b0ba6de1424 -r 2c0ca397d302 tool-data/salmon_indexes_versioned.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/salmon_indexes_versioned.loc.sample Sat Jul 27 12:37:47 2019 -0400 |
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| @@ -0,0 +1,32 @@ +# salmon_indexes_versioned.loc.sample +# This is a *.loc.sample file distributed with Galaxy that enables tools +# to use a directory of indexed data files. This one is for Salmon. +# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup +# First create these data files and save them in your own data directory structure. +# Then, create a salmon_indexes_versioned.loc.sample file to use those indexes with tools. +# Copy this file, save it with the same name (minus the .sample), +# follow the format examples, and store the result in this directory. +# The file should include an one line entry for each index set. +# The path points to the "basename" for the set, not a specific file. +# It has four text columns seperated by TABS. +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> <version> +# +# The <version> column can be retrieved from the header.json file in the index folder. e.g "IndexVersion": "q5" + + + +# So, for example, if you had sacCer3 indexes stored in: +# +# /depot/data2/galaxy/sacCer3/salmon_indexes/ +# +# then the salmon_indexes.loc entry could look like this: +# +#sacCer3 sacCer3 S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3) /depot/data2/galaxy/sacCer3/salmon_indexes/version_3/ q6 +# +#More examples: +# +#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/salmon_indexes/mm10/version_2 q4 +#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/salmon_indexes/dm3/version_1 q5 +# +# |
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| diff -r 6b0ba6de1424 -r 2c0ca397d302 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Thu Aug 23 15:58:26 2018 -0400 +++ b/tool_data_table_conf.xml.sample Sat Jul 27 12:37:47 2019 -0400 |
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| @@ -1,6 +1,7 @@ <tables> - <table name="salmon_indexes" comment_char="#"> - <columns>value, name, path</columns> - <file path="tool-data/salmon_indexes.loc" /> + <!-- Locations of indexes in salmon mapper format --> + <table name="salmon_indexes_versioned" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path, version</columns> + <file path="tool-data/salmon_indexes_versioned.loc" /> </table> </tables> |
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| diff -r 6b0ba6de1424 -r 2c0ca397d302 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Sat Jul 27 12:37:47 2019 -0400 |
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| @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of indexes in salmon mapper format --> + <table name="salmon_indexes_versioned" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path, version</columns> + <file path="${__HERE__}/test-data/cached_locally/salmon_indexes_versioned.loc" /> + </table> +</tables> |