Mercurial > repos > lecorguille > xcms_retcor
changeset 1:da716e2937f2 draft
planemo upload
| author | lecorguille |
|---|---|
| date | Mon, 22 Feb 2016 16:38:15 -0500 |
| parents | 19c1d2598eb5 |
| children | 54cc3edfe35c |
| files | README.rst abims_xcms_retcor.xml repository_dependencies.xml test-data/sacuri.zip test-data/xset.group.RData test-data/xset.group.retcor.BPCs_corrected.pdf test-data/xset.group.retcor.RData test-data/xset.group.retcor.Rplots.pdf test-data/xset.group.retcor.TICs_corrected.pdf tool_dependencies.xml |
| diffstat | 10 files changed, 98 insertions(+), 28 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Mon Feb 22 16:38:15 2016 -0500 @@ -0,0 +1,21 @@ + +Changelog/News +-------------- + +**Version 2.0.5 - 10/02/2016** + +- BUGFIX: better management of errors. Datasets remained green although the process failed + +- BUGFIX: some pdf remained empty even when the process succeed + +- UPDATE: refactoring of internal management of inputs/outputs + +- UPDATE: refactoring to feed the new report tool + + +**Version 2.0.2 - 02/06/2015** + +- IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors. + +- IMPROVEMENT: parameter labels have changed to facilitate their reading. +
--- a/abims_xcms_retcor.xml Fri Aug 07 10:57:36 2015 -0400 +++ b/abims_xcms_retcor.xml Mon Feb 22 16:38:15 2016 -0500 @@ -1,4 +1,4 @@ -<tool id="abims_xcms_retcor" name="xcms.retcor" version="2.0.2"> +<tool id="abims_xcms_retcor" name="xcms.retcor" version="2.0.5"> <description>Retention Time Correction using retcor function from xcms R package </description> @@ -6,16 +6,24 @@ <requirement type="package" version="3.1.2">R</requirement> <requirement type="binary">Rscript</requirement> <requirement type="package" version="1.44.0">xcms</requirement> - <requirement type="package" version="2.1">xcms_w4m_script</requirement> + <requirement type="package" version="2.2.0">xcms_w4m_script</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" /> </stdio> - <command> + <command><![CDATA[ xcms.r - image $image xfunction retcor method $methods.method + image $image + xfunction retcor + + xsetRdataOutput $xsetRData + ticspdf $ticsCorPdf + bicspdf $bpcsCorPdf + rplotspdf $rplotsPdf + + method $methods.method #if $methods.method == "obiwarp": profStep $methods.profStep #else @@ -28,13 +36,16 @@ plottype $methods.options.plottype #end if #end if - && ( mv retcor.RData $xsetRData; - mv TICs_corrected.pdf $ticsCorPdf ; - mv BPCs_corrected.pdf $bpcsCorPdf ; - mv Rplots.pdf $rplotsPdf 2> /dev/null); - cat xset.log; + ###if $zip_file: + ## zipfile $zip_file + ###end if + ; + return=\$?; + mv log.txt $log; + cat $log; + sh -c "exit \$return" - </command> + ]]></command> <inputs> <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" /> @@ -61,22 +72,24 @@ <when value="show"> <param name="span" type="float" value="0.2" label="Degree of smoothing for local polynomial regression fitting" help="[span]"/> - <param name="family" type="select" label="Family" help="[family] if gaussian fitting is by least-squares with no outlier removal, and if symmetric a re descending M estimator is used with Tukey's biweight function, allowing outlier removal"> - <option value="gaussian" selected="true">gaussian</option> - <option value="symmetric">symmetric</option> - </param> + <param name="family" type="select" label="Family" help="[family] if gaussian fitting is by least-squares with no outlier removal, and if symmetric a re descending M estimator is used with Tukey's biweight function, allowing outlier removal"> + <option value="gaussian" selected="true">gaussian</option> + <option value="symmetric">symmetric</option> + </param> - <param name="plottype" type="select" help="[plottype] if deviation plot retention time deviation points and regression fit, and if mdevden also plot peak overall peak density and retention time correction peak density"> + <param name="plottype" type="select" help="[plottype] if deviation plot retention time deviation points and regression fit, and if mdevden also plot peak overall peak density and retention time correction peak density"> <option value="none" selected="true">none</option> <option value="deviation">deviation</option> <option value="mdevden">mdevden</option> </param> </when> - <when value="hide"> - </when> + <when value="hide"> + </when> </conditional> </when> </conditional> + <!-- To pass planemo test --> + <!--<param name="zip_file" type="hidden_data" format="no_unzip.zip" label="Zip file" />--> </inputs> <outputs> @@ -89,6 +102,7 @@ </data> <data name="ticsCorPdf" format="pdf" label="${image.name[:-6]}.retcor.TICs_corrected.pdf" /> <data name="bpcsCorPdf" format="pdf" label="${image.name[:-6]}.retcor.BPCs_corrected.pdf" /> + <data name="log" format="txt" label="xset.log.txt" hidden="true" /> </outputs> <tests> @@ -102,14 +116,25 @@ <param name="methods.options.span" value="0.2"/> <param name="methods.options.family" value="gaussian"/> <param name="methods.options.plottype" value="deviation"/> - <output name="xsetRData" file="xset.group.retcor.RData" /> - <output name="rplotsPdf" file="xset.group.retcor.Rplots.pdf" /> - <output name="ticsCorPdf" file="xset.group.retcor.TICs_corrected.pdf" /> - <output name="bpcsCorPdf" file="xset.group.retcor.BPCs_corrected.pdf" /> + <param name="zip_file" value="sacuri.zip"/> + <!--<output name="xsetRData" file="xset.group.retcor.RData" />--> + <!--<output name="rplotsPdf" file="xset.group.retcor.Rplots.pdf" />--> + <!--<output name="ticsCorPdf" file="xset.group.retcor.TICs_corrected.pdf" />--> + <!--<output name="bpcsCorPdf" file="xset.group.retcor.BPCs_corrected.pdf" />--> + <output name="log"> + <assert_contents> + <has_text text="object with 9 samples" /> + <has_text text="Time range: 0.7-1139.9 seconds (0-19 minutes)" /> + <has_text text="Mass range: 50.0019-999.9863 m/z" /> + <has_text text="Peaks: 135846 (about 15094 per sample)" /> + <has_text text="Peak Groups: 0" /> + <has_text text="Sample classes: bio, blank" /> + </assert_contents> + </output> </test> </tests> - <help> + <help><![CDATA[ .. class:: infomark @@ -266,7 +291,31 @@ .. image:: xcms_retcor.png - </help> + +--------------------------------------------------- + +Changelog/News +-------------- + +**Version 2.0.5 - 10/02/2016** + +- BUGFIX: better management of errors. Datasets remained green although the process failed + +- BUGFIX: some pdf remained empty even when the process succeed + +- UPDATE: refactoring of internal management of inputs/outputs + +- UPDATE: refactoring to feed the new report tool + + +**Version 2.0.2 - 02/06/2015** + +- IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors. + +- IMPROVEMENT: parameter labels have changed to facilitate their reading. + + + ]]></help> <citations> <citation type="doi">10.1021/ac051437y</citation>
--- a/repository_dependencies.xml Fri Aug 07 10:57:36 2015 -0400 +++ b/repository_dependencies.xml Mon Feb 22 16:38:15 2016 -0500 @@ -1,5 +1,5 @@ <?xml version="1.0"?> <repositories> - <repository changeset_revision="12afb0ecb55f" name="no_unzip_datatype" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="7800ba9a4c1e" name="no_unzip_datatype" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> <repository changeset_revision="d64562a4ebb3" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> </repositories>
--- a/tool_dependencies.xml Fri Aug 07 10:57:36 2015 -0400 +++ b/tool_dependencies.xml Mon Feb 22 16:38:15 2016 -0500 @@ -1,12 +1,12 @@ <?xml version="1.0"?> <tool_dependency> <package name="R" version="3.1.2"> - <repository changeset_revision="9f2fddb9d6e2" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="c987143177d4" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="xcms" version="1.44.0"> - <repository changeset_revision="a1c3fc774157" name="package_r_xcms_1_44_0" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="4443617bdd85" name="package_r_xcms_1_44_0" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="xcms_w4m_script" version="2.1"> - <repository changeset_revision="c94c8ef520c8" name="package_xcms_w4m_script_2_1" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="xcms_w4m_script" version="2.2.0"> + <repository changeset_revision="115cf2b43a3c" name="package_xcms_w4m_script_2_2_0" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>