| Next changeset 1:e51ff83e4d94 (2015-11-24) |
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abims_xcms_group.xml repository_dependencies.xml static/images/xcms_group.png static/images/xcms_group_workflow.png test-data/xset.RData test-data/xset.group.RData test-data/xset.group.Rplots.pdf tool_dependencies.xml |
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| diff -r 000000000000 -r f3f97841564f abims_xcms_group.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abims_xcms_group.xml Fri Aug 07 11:02:28 2015 -0400 |
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| b'@@ -0,0 +1,266 @@\n+<tool id="abims_xcms_group" name="xcms.group" version="2.0.2">\n+\n+ <description>Group peaks together across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time.</description>\n+\n+ <requirements>\n+ <requirement type="package" version="3.1.2">R</requirement>\n+ <requirement type="binary">Rscript</requirement>\n+ <requirement type="package" version="1.44.0">xcms</requirement>\n+ <requirement type="package" version="2.1">xcms_w4m_script</requirement>\n+ </requirements>\n+\n+ <stdio>\n+ <exit_code range="1:" level="fatal" />\n+ </stdio>\n+\n+ <command>\n+ xcms.r \n+ xfunction group image $image method $methods.method sleep 0.001 \n+ #if $methods.method == "density":\n+ ## minsamp $methods.minsamp \n+ minfrac $methods.minfrac \n+ bw $methods.bw \n+ mzwid $methods.mzwid\n+ #if $methods.density_options.option == "show":\n+ max $methods.density_options.max\n+ #end if \n+ #elif $methods.method == "mzClust":\n+ mzppm $methods.mzppm\n+ mzabs $methods.mzabs\n+ minfrac $methods.minfrac\n+ ## minsamp $methods.minsamp\n+ #else:\n+ mzVsRTbalance $methods.mzVsRTbalance\n+ mzCheck $methods.mzCheck\n+ rtCheck $methods.rtCheck\n+ kNN $methods.kNN\n+ #end if\n+ && (\n+ mv group.RData $xsetRData;\n+ mv Rplots.pdf $rplotsPdf\n+ );\n+ cat xset.log\n+ </command> \n+\n+ <inputs>\n+ <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" />\n+ <conditional name="methods">\n+ <param name="method" type="select" label="Method to use for grouping" help="[method] See the help section below">\n+ <option value="density" selected="true">density</option>\n+ <option value="mzClust" >mzClust</option>\n+ <option value="nearest" >nearest</option>\n+ </param>\n+ <when value="density">\n+ <param name="bw" type="integer" value="30" label="Bandwidth" help="[bw] bandwidth (standard deviation or half width at half maximum) of gaussian smoothing kernel to apply to the peak density chromatogram" />\n+ <param name="minfrac" type="float" value="0.5" label="Minimum fraction of samples necessary" help="[minfrac] in at least one of the sample groups for it to be a valid group" />\n+ <param name="mzwid" type="float" value="0.25" label="Width of overlapping m/z slices" help="[mzwid] to use for creating peak density chromatograms and grouping peaks across samples " />\n+<!--\n+ <param name="minsamp" type="hidden" value="1" label="minsamp" help="minimum number of samples necessary in at least one of the sample groups for it to be a valid group " /> \n+-->\n+ <conditional name="density_options">\n+ <param name="option" type="select" label="Advanced options">\n+ <option value="show">show</option>\n+ <option value="hide" selected="true">hide</option>\n+ </param>\n+ <when value="show">\n+ <param name="max" type="integer" value="5" label="Maximum number of groups to identify in a single m/z slice" help="[max]" />\n+ </when>\n+ <when value="hide">\n+ </when>\n+ </conditional>\n+\n+ </when>\n+ <when value="mzClust">\n+ <param name="mzppm" type="integer" value="20 " label="Relative error used for clustering/grouping in ppm" help="[mzppm]" />\n+ <param name="mzabs" type="float" value="0" label="Absolute error used for clustering/grouping" help="[mzabs]" />\n+ <param name="minfrac" type="float" value="0" label="Minimum frac'..b'ort@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.\n+\n+\n+\n+---------------------------------------------------\n+\n+==========\n+Xcms.Group\n+==========\n+\n+-----------\n+Description\n+-----------\n+\n+After peak identification with xcmsSet, this tool groups the peaks which represent the same analyte across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time. Allows rejection of features, which are only partially detected within the replicates of a sample class.\n+\n+\n+\n+-----------------\n+Workflow position\n+-----------------\n+\n+**Upstream tools**\n+\n+========================= ================= =================== ==========\n+Name output file format parameter\n+========================= ================= =================== ==========\n+xcms.xcmsSet xset.RData rdata.xcms.raw RData file\n+------------------------- ----------------- ------------------- ----------\n+xcms.retcor xset.RData rdata.xcms.retcor RData file\n+========================= ================= =================== ==========\n+\n+\n+**Downstream tools**\n+\n++---------------------------+--------------------------------------+\n+| Name | Output file | Format |\n++===========================+=================+====================+\n+|xcms.retcor | xset.RData | rdata.xcms.group |\n++---------------------------+--------------------------------------+\n+|xcms.fillPeaks | xset.RData | rdata.xcms.group |\n++---------------------------+--------------------------------------+\n+\n+The output file is an xcmsSet.RData file. You can continue your analysis using it in **xcms.retcor** tool as an next step and then **xcms.fillPeaks**.\n+\n+**General schema of the metabolomic workflow**\n+\n+.. image:: xcms_group_workflow.png\n+\n+\n+-----------\n+Input files\n+-----------\n+\n++---------------------------+-----------------------+\n+| Parameter : num + label | Format |\n++===========================+=======================+\n+| 1 : RData file | rdata.xcms.group |\n++---------------------------+-----------------------+\n+\n+\n+----------\n+Parameters\n+----------\n+\n+Method to use for grouping\n+--------------------------\n+\n+**mzClust**\n+\n+ | Runs high resolution alignment on single spectra samples stored in the RData file generated by the **xcmsSet tool**.\n+\n+**density**\n+\n+ | Groups peaks together across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time.\n+\n+**nearest**\n+\n+ | Groups peaks together across samples by creating a master peak list and assigning corresponding peaks from all samples. It is inspired by the alignment algorithm of mzMine.\n+\n+\n+------------\n+Output files\n+------------\n+\n+xset.group.Rplots.pdf\n+\n+xset.group.RData: rdata.xcms.group format\n+\n+ | Rdata file that will be necessary in the third and fourth step of the workflow (xcms.retcor and xcms.fillpeaks).\n+ \n+\n+------\n+\n+.. class:: infomark \n+\n+The output file is an xset.group.RData file. You can continue your analysis using it in **xcms.retcor** tool.\n+\n+ \n+---------------------------------------------------\n+\n+\n+---------------\n+Working example\n+---------------\n+\n+Input files\n+-----------\n+\n+ | RData file -> **xset.RData**\n+\n+Parameters\n+----------\n+\n+ | Method -> **density**\n+ | bw -> **5**\n+ | minfrac -> **0.3**\n+ | mzwid -> **0.01**\n+ | Advanced options: **show**\n+ | max -> **50**\n+\n+\n+Output files\n+------------\n+\n+ | **1) xset.RData: RData file**\n+\n+ | **2) Example of an xset.group.Rplots pdf file**\n+\n+.. image:: xcms_group.png\n+ :width: 700\n+\n+\n+ </help>\n+\n+\n+ <citations>\n+ <citation type="doi">10.1021/ac051437y</citation>\n+ <citation type="doi">10.1093/bioinformatics/btu813</citation>\n+ </citations>\n+\n+\n+</tool>\n' |
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| diff -r 000000000000 -r f3f97841564f repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Fri Aug 07 11:02:28 2015 -0400 |
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| @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories> + <repository changeset_revision="d64562a4ebb3" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> +</repositories> |
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| diff -r 000000000000 -r f3f97841564f tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Aug 07 11:02:28 2015 -0400 |
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| @@ -0,0 +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" /> + </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" /> + </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> +</tool_dependency> |
