Mercurial > repos > lain > xseekerpreparator
changeset 4:8cc9fc8eacac draft
" master branch Updating"
| author | lain |
|---|---|
| date | Thu, 17 Dec 2020 12:54:10 +0000 |
| parents | fa97d16330be |
| children | 4d50e9324082 |
| files | XSeekerPreparator.xml galaxy/tools/LC-MSMS/XSeekerPreparator.xml |
| diffstat | 2 files changed, 32 insertions(+), 24 deletions(-) [+] |
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--- a/XSeekerPreparator.xml Thu Dec 17 10:13:58 2020 +0000 +++ b/XSeekerPreparator.xml Thu Dec 17 12:54:10 2020 +0000 @@ -10,16 +10,19 @@ </edam_operations> <requirements> - <requirement type="set_environment">R_SCRIPT</requirement> - <requirement type="package" version="4.0.0">R</requirement> - <requirement type="package" version="1.6.6">optparse</requirement> - <requirement type="package" version="3.10.2">xcms</requirement> - <requirement type="package" version="1.2.1">blob</requirement> - <requirement type="package" version="0.9.4">fst</requirement> - <requirement type="package" version="1.4.0">stringr</requirement> - <requirement type="package">DBModelR</requirement> + <requirement type="package" version="3.12.0">bioconductor-xcms</requirement> + <requirement type="package">bioconductor-camera</requirement> + <requirement type="package" version="2.29.2">git</requirement> + <requirement type="package" version="4.0">R</requirement> + <requirement type="package" version="1.2.1">r-blob</requirement> + <requirement type="package" version="1.1.0">r-dbi</requirement> + <requirement type="package" version="0.9.4">r-fst</requirement> + <requirement type="package" version="1.6.6">r-optparse</requirement> + <requirement type="package" version="1.4.0">r-stringr</requirement> + <requirement type="package" version="0.3.4">r-purrr</requirement> + <requirement type="package" version="2.2.1">r-rsqlite</requirement> + <requirement type="package" version="0.1.0">r-dbmodelr</requirement> </requirements> - <stdio> <exit_code @@ -37,12 +40,12 @@ </stdio> <version_command> - $R_SCRIPT '$__tool_directory__/XSeekerPreparator.R' -v + Rscript '$__tool_directory__/XSeekerPreparator.R' -v </version_command> <command> <![CDATA[ - $R_SCRIPT '$__tool_directory__/XSeekerPreparator.R' + Rscript '$__tool_directory__/XSeekerPreparator.R' -P @@ -50,7 +53,7 @@ --output '$output' #if $samples.selected - --samples '${",".join(samples.selected)}' + --samples '${",".join($samples.selected)}' #end if #if $database.archetypes @@ -155,6 +158,7 @@ <outputs> <data format="sqlite" name="output" /> + <!-- <data format="xseeker.sqlite" name="output" /> --> </outputs> <configfiles>
--- a/galaxy/tools/LC-MSMS/XSeekerPreparator.xml Thu Dec 17 10:13:58 2020 +0000 +++ b/galaxy/tools/LC-MSMS/XSeekerPreparator.xml Thu Dec 17 12:54:10 2020 +0000 @@ -10,16 +10,19 @@ </edam_operations> <requirements> - <requirement type="set_environment">R_SCRIPT</requirement> - <requirement type="package" version="4.0.0">R</requirement> - <requirement type="package" version="1.6.6">optparse</requirement> - <requirement type="package" version="3.10.2">xcms</requirement> - <requirement type="package" version="1.2.1">blob</requirement> - <requirement type="package" version="0.9.4">fst</requirement> - <requirement type="package" version="1.4.0">stringr</requirement> - <requirement type="package">DBModelR</requirement> + <requirement type="package" version="3.12.0">bioconductor-xcms</requirement> + <requirement type="package">bioconductor-camera</requirement> + <requirement type="package" version="2.29.2">git</requirement> + <requirement type="package" version="4.0">R</requirement> + <requirement type="package" version="1.2.1">r-blob</requirement> + <requirement type="package" version="1.1.0">r-dbi</requirement> + <requirement type="package" version="0.9.4">r-fst</requirement> + <requirement type="package" version="1.6.6">r-optparse</requirement> + <requirement type="package" version="1.4.0">r-stringr</requirement> + <requirement type="package" version="0.3.4">r-purrr</requirement> + <requirement type="package" version="2.2.1">r-rsqlite</requirement> + <requirement type="package" version="0.1.0">r-dbmodelr</requirement> </requirements> - <stdio> <exit_code @@ -37,12 +40,12 @@ </stdio> <version_command> - $R_SCRIPT '$__tool_directory__/XSeekerPreparator.R' -v + Rscript '$__tool_directory__/XSeekerPreparator.R' -v </version_command> <command> <![CDATA[ - $R_SCRIPT '$__tool_directory__/XSeekerPreparator.R' + Rscript '$__tool_directory__/XSeekerPreparator.R' -P @@ -50,7 +53,7 @@ --output '$output' #if $samples.selected - --samples '${",".join(samples.selected)}' + --samples '${",".join($samples.selected)}' #end if #if $database.archetypes @@ -155,6 +158,7 @@ <outputs> <data format="sqlite" name="output" /> + <!-- <data format="xseeker.sqlite" name="output" /> --> </outputs> <configfiles>