Mercurial > repos > lecorguille > camera_annotate
changeset 8:8c5bb7b86df9 draft
planemo upload
author | lecorguille |
---|---|
date | Mon, 22 Feb 2016 16:48:11 -0500 (2016-02-22) |
parents | 9882346d42a8 |
children | 7da9252dd983 |
files | Makefile README.rst abims_CAMERA_annotateDiffreport.xml tool_dependencies.xml |
diffstat | 4 files changed, 109 insertions(+), 25 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Makefile Mon Feb 22 16:48:11 2016 -0500 @@ -0,0 +1,23 @@ +# USAGE: make [install|clean] + +# -------- VARIABLE -------- + +OBJ=camera_annotate.tgz +DEP=abims_CAMERA_annotateDiffreport.xml tool_dependencies.xml repository_dependencies.xml static test-data + + +# ------------------------ + +all: $(OBJ) + +$(OBJ): $(DEP) + tar --exclude=".svn" -zchf $@ $^ + +# ------------------------ + +install: $(OBJ) + mv *.tgz ~ + +clean: + rm *.tgz +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Mon Feb 22 16:48:11 2016 -0500 @@ -0,0 +1,29 @@ + +Changelog/News +-------------- + +**Version 2.1.3 - 10/02/2016** + +- BUGFIX: better management of errors. Datasets remained green although the process failed + +- BUGFIX: the conversion into minutes of the retention time was applied to the diffreport outputs (several conditions) + +- IMPROVEMENT: when there are several conditions, the tool will generate individual datasets (tsv, pdf) instead of a zip file. The usual png (eic, boxplot) will from now be integrated in two pdf. + +- UPDATE: refactoring of internal management of inputs/outputs + + +VERSION 2.1.0 - 09/10/2015** + +- BUGFIX: There was a bug with the CAMERA.annotate (generating a bad dataMatrix (intensities which don't match with the metabolites)) + + +VERSION 2.1.0 - 07/06/2015** + +- IMPROVEMENT: new datatype/dataset formats (rdata.camera.positive, rdata.camera.negative, rdata.camera.quick ...) will facilitate the sequence of tools and so avoid incompatibility errors. + +- IMPROVEMENT: parameter labels have changed to facilitate their reading. + +- UPDATE: merged with annotateDiffreport. Some parameters are dedicated to experiences with several conditions + +
--- a/abims_CAMERA_annotateDiffreport.xml Thu Dec 17 09:09:41 2015 -0500 +++ b/abims_CAMERA_annotateDiffreport.xml Mon Feb 22 16:48:11 2016 -0500 @@ -1,4 +1,4 @@ -<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.1.0"> +<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.1.3"> <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description> @@ -7,17 +7,27 @@ <requirement type="binary">Rscript</requirement> <requirement type="package" version="1.44.0">xcms</requirement> <requirement type="package" version="1.22.0">camera</requirement> - <requirement type="package" version="2.1">camera_w4m_script</requirement> + <requirement type="package" version="2.2.1">camera_w4m_script</requirement> + <requirement type="binary">CAMERA.r</requirement> + <requirement type="package" version="1.3.18">graphicsmagick</requirement> + <requirement type="binary">convert</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" /> </stdio> - <command interpreter="Rscript"> + <command><![CDATA[ CAMERA.r - xfunction annotatediff image $image - convert_param $convert_param num_digits $num_digits nSlaves \${GALAXY_SLOTS:-1} + xfunction annotatediff + image $image + + variableMetadataOutput $variableMetadata + dataMatrixOutput $datamatrix + xsetRdataOutput $rdata + + convert_param $convert_param num_digits $num_digits + nSlaves \${GALAXY_SLOTS:-1} sigma $sigma perfwhm $perfwhm maxcharge $maxcharge maxiso $maxiso minfrac $minfrac ppm $ppm mzabs $mzabs intval $intval @@ -35,6 +45,7 @@ #end if #if $options.option == "show": + runDiffreport TRUE eicmax $options.eicmax eicwidth $options.eicwidth value $options.value @@ -42,24 +53,11 @@ h $options.h w $options.w mzdec $options.mzdec - #else - eicmax 0 - eicwidth 200 - value "into" - sortpval TRUE - h 480 - w 640 - mzdec 2 + new_file_path ${__new_file_path__}/primary_${output_diffreport.id}_ #end if - && ( - mv variableMetadata.tsv $variableMetadata; - mv dataMatrix.tsv $datamatrix; - mv annotatediff.RData $rdata - ); - cat xset.log - </command> + ]]></command> <inputs> @@ -145,7 +143,7 @@ <when input="quick_block.polarity" value="negative" format="rdata.camera.negative" /> </change_format> </data> - <data name="output_zip" format="zip" from_work_dir="Xdiffreport.zip" label="${image.name[:-6]}.annotateDiffreport.zip" > + <data name="output_diffreport" format="text" label="${image.name[:-6]}.annotateDiffreport" hidden="True"> <filter>(options['option'] == 'show')</filter> </data> </outputs> @@ -189,7 +187,7 @@ - <help> + <help><![CDATA[ .. class:: infomark @@ -374,7 +372,38 @@ .. image:: annotatediffreport_variableMetadata.png - </help> + +--------------------------------------------------- + +Changelog/News +-------------- + +**Version 2.1.3 - 10/02/2016** + +- BUGFIX: better management of errors. Datasets remained green although the process failed + +- BUGFIX: the conversion into minutes of the retention time was applied to the diffreport outputs (several conditions) + +- IMPROVEMENT: when there are several conditions, the tool will generate individual datasets (tsv, pdf) instead of a zip file. The usual png (eic, boxplot) will from now be integrated in two pdf. + +- UPDATE: refactoring of internal management of inputs/outputs + + +VERSION 2.1.0 - 09/10/2015** + +- BUGFIX: There was a bug with the CAMERA.annotate (generating a bad dataMatrix (intensities which don't match with the metabolites)) + + +VERSION 2.1.0 - 07/06/2015** + +- IMPROVEMENT: new datatype/dataset formats (rdata.camera.positive, rdata.camera.negative, rdata.camera.quick ...) will facilitate the sequence of tools and so avoid incompatibility errors. + +- IMPROVEMENT: parameter labels have changed to facilitate their reading. + +- UPDATE: merged with annotateDiffreport. Some parameters are dedicated to experiences with several conditions + + + ]]></help> <citations> <citation type="doi">10.1021/ac202450g</citation>
--- a/tool_dependencies.xml Thu Dec 17 09:09:41 2015 -0500 +++ b/tool_dependencies.xml Mon Feb 22 16:48:11 2016 -0500 @@ -6,7 +6,10 @@ <package name="camera" version="1.22.0"> <repository changeset_revision="845eb883bd1b" name="package_r_camera_1_22_0" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="camera_w4m_script" version="2.1"> - <repository changeset_revision="208bc3eea24c" name="package_camera_w4m_script_2_1" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="camera_w4m_script" version="2.2.1"> + <repository changeset_revision="91b0d23c9d52" name="package_camera_w4m_script_2_2_1" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="graphicsmagick" version="1.3.18"> + <repository changeset_revision="ef238a8bdc1d" name="package_graphicsmagick_1_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>