Mercurial > repos > lecorguille > xcms_fillpeaks
changeset 16:34fe699200ce draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 878be1bfbe93af0a140df76fa47f0a82a48189e3
| author | lecorguille |
|---|---|
| date | Tue, 09 Oct 2018 04:42:22 -0400 |
| parents | 1b60d8eb704a |
| children | b6b62413936f |
| files | README.rst abims_xcms_fillPeaks.xml macros_xcms.xml |
| diffstat | 3 files changed, 28 insertions(+), 7 deletions(-) [+] |
line wrap: on
line diff
--- a/README.rst Thu Oct 04 10:38:22 2018 -0400 +++ b/README.rst Tue Oct 09 04:42:22 2018 -0400 @@ -2,6 +2,11 @@ Changelog/News -------------- +**Version 3.0.0.1 - 09/10/2018** + +- IMPROVEMENT: the export of the PeakList is now mandatory + + **Version 3.0.0.0 - 08/03/2018** - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods. Some parameters may have been renamed.
--- a/abims_xcms_fillPeaks.xml Thu Oct 04 10:38:22 2018 -0400 +++ b/abims_xcms_fillPeaks.xml Tue Oct 09 04:42:22 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="abims_xcms_fillPeaks" name="xcms fillChromPeaks (fillPeaks)" version="@WRAPPER_VERSION@.0"> +<tool id="abims_xcms_fillPeaks" name="xcms fillChromPeaks (fillPeaks)" version="@WRAPPER_VERSION@.1"> <description>Integrate areas of missing peaks</description> @@ -37,7 +37,7 @@ <param argument="ppm" type="integer" value="0" label="Specifying a ppm by which the mz width of the peak region should be expanded" help="For peaks with an mz width smaller than ‘mean(c(mzmin, mzmax)) * ppm / 1e6’, the ‘mzmin’ will be replaced by ‘mean(c(mzmin, mzmax)) - (mean(c(mzmin, mzmax)) * ppm / 2 / 1e6)’ and ‘mzmax’ by ‘mean(c(mzmin, mzmax)) + (mean(c(mzmin, mzmax)) * ppm / 2 / 1e6)’. This is applied before eventually expanding the mz width using the ‘expandMz’ parameter." /> </section> - <expand macro="input_peaklist"/> + <expand macro="input_peaklist_section"/> <expand macro="input_file_load"/> @@ -130,12 +130,12 @@ </test>--> <test> <param name="image" value="faahKO-single.xset.merged.group2.retcor2.group2.RData" ftype="rdata"/> - <conditional name="peaklist"> + <section name="peaklist"> <param name="peaklistBool" value="true" /> <param name="convertRTMinute" value="false" /> <param name="numDigitsMZ" value="4" /> <param name="numDigitsRT" value="1" /> - </conditional> + </section> <expand macro="test_file_load_single"/> <assert_stdout> <has_text text="expandMz: 0" /> @@ -230,6 +230,11 @@ Changelog/News -------------- +**Version 3.0.0.1 - 09/10/2018** + +- IMPROVEMENT: the export of the PeakList is now mandatory + + **Version 3.0.0.0 - 08/03/2018** - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods. Some parameters may have been renamed.
--- a/macros_xcms.xml Thu Oct 04 10:38:22 2018 -0400 +++ b/macros_xcms.xml Tue Oct 09 04:42:22 2018 -0400 @@ -90,9 +90,6 @@ </token> <xml name="input_peaklist"> - <conditional name="peaklist"> - <param name="peaklistBool" type="boolean" label="Get a Peak List" /> - <when value="true"> <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/> <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" /> <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" /> @@ -102,6 +99,20 @@ <option value="intb">intb</option> </param> <param name="naTOzero" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Replace the remain NA by 0 in the dataMatrix" help="Rather mandatory for some downstream statistical steps"/> + </xml> + + <xml name="input_peaklist_section"> + <section name="peaklist" title="Peak List" expanded="True"> + <param name="peaklistBool" type="hidden" label="Get the Peak List" value="True" /> + <expand macro="input_peaklist"/> + </section> + </xml> + + <xml name="input_peaklist_conditional"> + <conditional name="peaklist"> + <param name="peaklistBool" type="boolean" label="Get the Peak List" /> + <when value="true"> + <expand macro="input_peaklist"/> </when> <when value="false" /> </conditional>