Mercurial > repos > artbio > xpore
changeset 1:ff53cf0d0bbd draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 8a69e869b86c4c371c18e7fde1e6b6af41f315a4"
author | artbio |
---|---|
date | Fri, 28 May 2021 23:32:25 +0000 (2021-05-28) |
parents | b64b9a2bf4f0 |
children | a5758bb680c8 |
files | xpore_dataprep.xml xpore_diffmod.xml |
diffstat | 2 files changed, 23 insertions(+), 16 deletions(-) [+] |
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--- a/xpore_dataprep.xml Wed May 26 23:14:24 2021 +0000 +++ b/xpore_dataprep.xml Fri May 28 23:32:25 2021 +0000 @@ -1,8 +1,7 @@ -<tool id="xpore_dataprep" name="xpore-dataprep" version="0.5.6+galaxy1"> +<tool id="xpore_dataprep" name="xpore-dataprep" version="0.5.6+galaxy2"> <description></description> <requirements> <requirement type="package" version="0.5.6">xpore</requirement> - <requirement type="package" version="1.9.0">pyensembl</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Tool exception" /> @@ -13,7 +12,14 @@ --summary '$eventalign_summary' --out_dir out --n_processes \${GALAXY_SLOTS:-4} && - ls -la out + mv ./out/data.index $data_index && + mv ./out/eventalign.hdf5 $eventalign_hdf5 && + mv ./out/data.log $data_log && + mv ./out/eventalign.log $eventalign_log && + mv ./out/data.readcount $data_readcount && + mv ./out/data.json $data_json + + ]]></command> <inputs> <param name="eventalign_reads" type="data" format="txt,tabular" label="aligned nanopore events" @@ -23,12 +29,12 @@ </inputs> <outputs> - <data format="txt" name="data_index" label="data.index" from_work_dir="./out/data.index" /> - <data format="h5" name="eventalign_hdf5" label="eventalign.hdf5" from_work_dir="./out/eventalign.hdf5" /> - <data format="txt" name="data_log" label="data.log" from_work_dir="./out/data.log" /> - <data format="txt" name="eventalign_log" label="eventalign.log" from_work_dir="./out/eventalign.log" /> - <data format="txt" name="data_readcount" label="data.readcount" from_work_dir="./out/data.readcount" /> - <data format="json" name="data_json" label="data.json" from_work_dir="./out/data.json"/> + <data format="txt" name="data_index" label="data.index" /> + <data format="h5" name="eventalign_hdf5" label="eventalign.hdf5" /> + <data format="txt" name="data_log" label="data.log" /> + <data format="txt" name="eventalign_log" label="eventalign.log" /> + <data format="txt" name="data_readcount" label="data.readcount" /> + <data format="json" name="data_json" label="data.json" /> </outputs> <tests>
--- a/xpore_diffmod.xml Wed May 26 23:14:24 2021 +0000 +++ b/xpore_diffmod.xml Fri May 28 23:32:25 2021 +0000 @@ -1,8 +1,7 @@ -<tool id="xpore_diffmod" name="xpore-diffmod" version="0.5.6+galaxy1"> +<tool id="xpore_diffmod" name="xpore-diffmod" version="0.5.6+galaxy2"> <description></description> <requirements> <requirement type="package" version="0.5.6">xpore</requirement> - <requirement type="package" version="1.9.0">pyensembl</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Tool exception" /> @@ -31,9 +30,11 @@ printf " prefiltering:\n" >> config.yml && printf " method: t-test\n" >> config.yml && printf " threshold: 0.1\n" >> config.yml && - xpore-diffmod --config config.yml --n_processes \${GALAXY_SLOTS:-4} && - sed -i "s/,/\t/g" ./out/diffmod.table + sed -i "s/,/\t/g" ./out/diffmod.table && + mv ./out/diffmod.table $diffmod_table && + mv ./out/diffmod.log $diffmod_log && + mv ./config.yml $config ]]></command> <inputs> @@ -64,9 +65,9 @@ </inputs> <outputs> - <data format="tabular" name="diffmod_table" label="diffmod table" from_work_dir="./out/diffmod.table" /> - <data format="txt" name="diffmod_log" label="diffmod log" from_work_dir="./out/diffmod.log" /> - <data format="txt" name="config" label="configuration.yml" from_work_dir="./config.yml" /> + <data format="tabular" name="diffmod_table" label="diffmod table" /> + <data format="txt" name="diffmod_log" label="diffmod log" /> + <data format="txt" name="config" label="configuration.yml" /> </outputs> <tests> <test>