Mercurial > repos > youyuh48 > centrifuge_kreport
changeset 0:d4372c7fa79d draft
planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/centrifuge
| author | youyuh48 |
|---|---|
| date | Thu, 30 Aug 2018 08:39:45 -0400 |
| parents | |
| children | ccb90fac3605 |
| files | centrifuge_kreport.xml test-data/centrifuge_indices.loc test-data/centrifuge_test.1.cf test-data/centrifuge_test.2.cf test-data/centrifuge_test.3.cf test-data/defaults.tsv test-data/defaults.tsv.kreport tool-data/centrifuge_indices.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
| diffstat | 10 files changed, 144 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/centrifuge_kreport.xml Thu Aug 30 08:39:45 2018 -0400 @@ -0,0 +1,48 @@ +<tool id="centrifuge_kreport" name="centrifuge_kreport" version="0.1.0"> + <description>Centrifuge-kreport creates Kraken-style reports from centrifuge out files</description> + <requirements> + <requirement type="package" version="1.0.3">centrifuge</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + centrifuge-kreport + -x '${db.fields.path}' + $input > output.txt + ]]></command> + <inputs> + <param type="data" name="input" format="tabular" /> + <param name="db" type="select" label="Select a reference database"> + <options from_data_table="centrifuge_indices"> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="No indexes are available for the selected input dataset"/> + </options> + </param> + </inputs> + <outputs> + <data format="tsv" name="output" from_work_dir="output.txt" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test> + <param name="input" value="test-data_centrifuge-kreport/defaults.tsv"/> + <output name="output" file="defaults.tsv.kreport"/> + </test> + </tests> + <help><![CDATA[ +Usage: centrifuge-kreport -x <index name> OPTIONS <centrifuge output file(s)> + +centrifuge-kreport creates Kraken-style reports from centrifuge out files. + +Options: + -x INDEX (REQUIRED) Centrifuge index + + --only-unique Only count reads that were uniquely assigned to one taxon + --show-zeros Show clades that have zero reads, too + --is-count-table The format of the file is 'TAXID<tab>COUNT' instead of the standard + Centrifuge output format + + --min-score SCORE Require a minimum score for reads to be counted + --min-length LENGTH Require a minimum alignment length to the read + ]]></help> + <citations> + <citation type="doi">10.1101/gr.210641.116</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/centrifuge_indices.loc Thu Aug 30 08:39:45 2018 -0400 @@ -0,0 +1,15 @@ +# centrifuge_indices.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 GOTTCHA. +# 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 bowtie_indices.loc 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 three text columns seperated by TABS. +# +# <unique_id> <display_name> <file_base_path> +# +test test ${__HERE__}/centrifuge_test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/defaults.tsv Thu Aug 30 08:39:45 2018 -0400 @@ -0,0 +1,17 @@ +readID seqID taxID score 2ndBestScore hitLength queryLength numMatches +C_1 gi|7 9913 4225 4225 80 80 2 +C_1 gi|4 9646 4225 4225 80 80 2 +C_2 gi|4 9646 4225 4225 80 80 2 +C_2 gi|7 9913 4225 4225 80 80 2 +C_3 gi|7 9913 4225 4225 80 80 2 +C_3 gi|4 9646 4225 4225 80 80 2 +C_4 gi|4 9646 4225 4225 80 80 2 +C_4 gi|7 9913 4225 4225 80 80 2 +1_1 gi|4 9646 4225 0 80 80 1 +1_2 gi|4 9646 4225 0 80 80 1 +2_1 gi|7 9913 4225 0 80 80 1 +2_2 gi|7 9913 4225 0 80 80 1 +2_3 gi|7 9913 4225 0 80 80 1 +2_4 gi|7 9913 4225 0 80 80 1 +2_5 gi|7 9913 4225 0 80 80 1 +2_6 gi|7 9913 4225 0 80 80 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/defaults.tsv.kreport Thu Aug 30 08:39:45 2018 -0400 @@ -0,0 +1,36 @@ + 0.00 0 0 U 0 unclassified + 75.00 12 0 - 1 root + 75.00 12 0 - 131567 cellular organisms + 75.00 12 0 D 2759 Eukaryota + 75.00 12 0 - 33154 Opisthokonta + 75.00 12 0 K 33208 Metazoa + 75.00 12 0 - 6072 Eumetazoa + 75.00 12 0 - 33213 Bilateria + 75.00 12 0 - 33511 Deuterostomia + 75.00 12 0 P 7711 Chordata + 75.00 12 0 - 89593 Craniata + 75.00 12 0 - 7742 Vertebrata + 75.00 12 0 - 7776 Gnathostomata + 75.00 12 0 - 117570 Teleostomi + 75.00 12 0 - 117571 Euteleostomi + 75.00 12 0 - 8287 Sarcopterygii + 75.00 12 0 - 1338369 Dipnotetrapodomorpha + 75.00 12 0 - 32523 Tetrapoda + 75.00 12 0 - 32524 Amniota + 75.00 12 0 C 40674 Mammalia + 75.00 12 0 - 32525 Theria + 75.00 12 0 - 9347 Eutheria + 75.00 12 0 - 1437010 Boreoeutheria + 75.00 12 0 - 314145 Laurasiatheria + 50.00 8 0 - 91561 Cetartiodactyla + 50.00 8 0 - 9845 Ruminantia + 50.00 8 0 - 35500 Pecora + 50.00 8 0 F 9895 Bovidae + 50.00 8 0 - 27592 Bovinae + 50.00 8 0 G 9903 Bos + 50.00 8 8 S 9913 Bos taurus + 25.00 4 0 O 33554 Carnivora + 25.00 4 0 - 379584 Caniformia + 25.00 4 0 F 9632 Ursidae + 25.00 4 0 G 9645 Ailuropoda + 25.00 4 4 S 9646 Ailuropoda melanoleuca
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/centrifuge_indices.loc.sample Thu Aug 30 08:39:45 2018 -0400 @@ -0,0 +1,15 @@ +# centrifuge_indices.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 GOTTCHA. +# 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 bowtie_indices.loc 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 three text columns seperated by TABS. +# +# <unique_id> <display_name> <file_base_path> +# +#p_compressed p_compressed_2018_4_15 /galaxy-central/tool-data/centrifuge/p_compressed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Aug 30 08:39:45 2018 -0400 @@ -0,0 +1,7 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <table name="centrifuge_indices" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/centrifuge_indices.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Thu Aug 30 08:39:45 2018 -0400 @@ -0,0 +1,6 @@ +<tables> + <table name="centrifuge_indices" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/test-data/centrifuge_indices.loc" /> + </table> +</tables>