| Previous changeset 2:5815e6e11f9b (2015-11-24) Next changeset 4:2edfa5e1f719 (2016-04-08) |
|
Commit message:
planemo upload |
|
modified:
abims_xcms_fillPeaks.xml repository_dependencies.xml test-data/xset.group.retcor.group.RData test-data/xset.group.retcor.group.fillPeaks.RData tool_dependencies.xml |
|
added:
README.rst test-data/log.txt test-data/sacuri.zip |
| b |
| diff -r 5815e6e11f9b -r 5a54397dbc97 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Mon Feb 22 16:40:19 2016 -0500 |
| b |
| @@ -0,0 +1,19 @@ + +Changelog/News +-------------- + +**Version 2.0.5 - 10/02/2016** + +- BUGFIX: better management of errors. Datasets remained green although the process failed + +- 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. + |
| b |
| diff -r 5815e6e11f9b -r 5a54397dbc97 abims_xcms_fillPeaks.xml --- a/abims_xcms_fillPeaks.xml Tue Nov 24 06:26:14 2015 -0500 +++ b/abims_xcms_fillPeaks.xml Mon Feb 22 16:40:19 2016 -0500 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.0.2"> +<tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.0.5"> <description>Integrate the signal in the region of that peak group not represented and create a new peak</description> @@ -6,16 +6,32 @@ <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> - xcms.r xfunction fillPeaks image $image method $method && mv fillPeaks.RData $xsetRData; cat xset.log - </command> + <command><![CDATA[ + xcms.r + xfunction fillPeaks + image $image + + xsetRdataOutput $xsetRData + + method $method + + ###if $zip_file: + ## zipfile $zip_file + ###end if + ; + return=\$?; + mv log.txt $log; + cat $log; + sh -c "exit \$return" + + ]]></command> <inputs> <param name="image" type="data" format="rdata.xcms.group,rdata" label="xset RData file" help="output file from another function xcms (group)" /> @@ -23,21 +39,35 @@ <option value="chrom" selected="true">chrom</option> <option value="MSW" >MSW</option> </param> + <!-- To pass planemo test --> + <!--<param name="zip_file" type="hidden_data" format="no_unzip.zip" label="Zip file" />--> </inputs> <outputs> <data name="xsetRData" format="rdata.xcms.fillpeaks" label="${image.name[:-6]}.fillPeaks.RData" /> + <data name="log" format="txt" label="xset.log.txt" hidden="true" /> </outputs> <tests> <test> <param name="image" value="xset.group.retcor.group.RData"/> <param name="method" value="chrom"/> - <output name="xsetRData" file="xset.group.retcor.group.fillPeaks.RData" /> + <param name="zip_file" value="sacuri.zip"/> + <!--<output name="xsetRData" file="xset.group.retcor.group.fillPeaks.RData" />--> + <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: 157780 (about 17531 per sample)" /> + <has_text text="Peak Groups: 6761" /> + <has_text text="Sample classes: bio, blank" /> + </assert_contents> + </output> </test> </tests> - <help> + <help><![CDATA[ .. class:: infomark @@ -172,9 +202,28 @@ | **xset.fillPeaks.RData: RData file** +--------------------------------------------------- + +Changelog/News +-------------- + +**Version 2.0.5 - 10/02/2016** + +- BUGFIX: better management of errors. Datasets remained green although the process failed + +- UPDATE: refactoring of internal management of inputs/outputs + +- UPDATE: refactoring to feed the new report tool - </help> +**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> |
| b |
| diff -r 5815e6e11f9b -r 5a54397dbc97 repository_dependencies.xml --- a/repository_dependencies.xml Tue Nov 24 06:26:14 2015 -0500 +++ b/repository_dependencies.xml Mon Feb 22 16:40:19 2016 -0500 |
| b |
| @@ -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> |
| b |
| diff -r 5815e6e11f9b -r 5a54397dbc97 test-data/log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/log.txt Mon Feb 22 16:40:19 2016 -0500 |
| b |
| @@ -0,0 +1,55 @@ + PACKAGE INFO +parallel 3.1.2 +BiocGenerics 0.14.0 +Biobase 2.28.0 +Rcpp 0.12.0 +mzR 2.2.2 +xcms 1.44.0 +snow 0.3.13 +batch 1.1.4 + + + ARGUMENTS INFO +xfunction fillPeaks +image test-data/xset.group.retcor.group.RData +xsetRdataOutput test-data/xset.group.retcor.group.fillPeaks.RData +method chrom +zipfile test-data/sacuri.zip + + + INFILE PROCESSING INFO + + + ARGUMENTS PROCESSING INFO + + + MAIN PROCESSING INFO +./sacuri/bio/HU_neg_028.mzXML +./sacuri/bio/HU_neg_060.mzXML +./sacuri/bio/HU_neg_051.mzXML +./sacuri/bio/HU_neg_017.mzXML +./sacuri/bio/HU_neg_034.mzXML +./sacuri/blank/Blanc09.mzXML +./sacuri/blank/Blanc06.mzXML +./sacuri/blank/Blanc12.mzXML +./sacuri/blank/Blanc04.mzXML +null device + 1 + + + XSET OBJECT INFO +An "xcmsSet" object with 9 samples + +Time range: 0.7-1139.9 seconds (0-19 minutes) +Mass range: 50.0019-999.9863 m/z +Peaks: 157780 (about 17531 per sample) +Peak Groups: 6761 +Sample classes: bio, blank + +Profile settings: method = bin + step = 0.01 + +Memory usage: 17.4 MB + + + DONE |
| b |
| diff -r 5815e6e11f9b -r 5a54397dbc97 test-data/sacuri.zip |
| b |
| Binary file test-data/sacuri.zip has changed |
| b |
| diff -r 5815e6e11f9b -r 5a54397dbc97 test-data/xset.group.retcor.group.RData |
| b |
| Binary file test-data/xset.group.retcor.group.RData has changed |
| b |
| diff -r 5815e6e11f9b -r 5a54397dbc97 test-data/xset.group.retcor.group.fillPeaks.RData |
| b |
| Binary file test-data/xset.group.retcor.group.fillPeaks.RData has changed |
| b |
| diff -r 5815e6e11f9b -r 5a54397dbc97 tool_dependencies.xml --- a/tool_dependencies.xml Tue Nov 24 06:26:14 2015 -0500 +++ b/tool_dependencies.xml Mon Feb 22 16:40:19 2016 -0500 |
| b |
| @@ -6,7 +6,7 @@ <package name="xcms" version="1.44.0"> <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> |