| Next changeset 1:44df3679bb3d (2015-08-07) |
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Commit message:
planemo upload |
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added:
Makefile abims_CAMERA_annotateDiffreport.xml planemo.sh repository_dependencies.xml static/images/annotate_workflow.png static/images/annotatediffreport_box.png static/images/annotatediffreport_box1.png static/images/annotatediffreport_dataMatrix.png static/images/annotatediffreport_eic.png static/images/annotatediffreport_eic1.png static/images/annotatediffreport_variableMetadata.png static/images/annotatediffreport_workflow.png test-data/xset.group.retcor.group.fillPeaks.RData test-data/xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv test-data/xset.group.retcor.group.fillPeaks.annotate.negative.Rdata test-data/xset.group.retcor.group.fillPeaks.annotate.variableMetadata.Xdiffreport.zip test-data/xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv tool_dependencies.xml |
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| diff -r 000000000000 -r e0afb8854cc4 Makefile --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Makefile Fri Aug 07 11:08:16 2015 -0400 |
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| @@ -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 + |
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| diff -r 000000000000 -r e0afb8854cc4 abims_CAMERA_annotateDiffreport.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abims_CAMERA_annotateDiffreport.xml Fri Aug 07 11:08:16 2015 -0400 |
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| b'@@ -0,0 +1,386 @@\n+<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.0.1">\n+\n+ <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</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="1.22.0">camera</requirement>\n+ <requirement type="package" version="2.1">camera_w4m_script</requirement>\n+ </requirements>\n+ \n+ <stdio>\n+ <exit_code range="1:" level="fatal" />\n+ </stdio>\n+\n+ <command>\n+ CAMERA.r \n+ xfunction annotatediff image $image\n+ convert_param $convert_param num_digits $num_digits nSlaves \\${GALAXY_SLOTS:-1}\n+ sigma $sigma perfwhm $perfwhm \n+ maxcharge $maxcharge maxiso $maxiso minfrac $minfrac\n+ ppm $ppm mzabs $mzabs intval $intval \n+ max_peaks $max_peaks\n+ quick $quick_block.quick\n+ #if $quick_block.quick == "FALSE"\n+ polarity $quick_block.polarity\n+ cor_eic_th $quick_block.cor_eic_th\n+ graphMethod $quick_block.graphMethod \n+ pval $quick_block.pval \n+ calcCiS $quick_block.calcCiS\n+ calcIso $quick_block.calcIso\n+ calcCaS $quick_block.calcCaS\n+ multiplier $quick_block.multiplier\n+ #end if\n+\n+ #if $options.option == "show":\n+ eicmax $options.eicmax\n+ eicwidth $options.eicwidth\n+ value $options.value\n+ sortpval $options.sortpval \n+ h $options.h\n+ w $options.w\n+ mzdec $options.mzdec\n+ #else\n+ eicmax 0\n+ eicwidth 200\n+ value "into"\n+ sortpval TRUE \n+ h 480\n+ w 640\n+ mzdec 2\n+ #end if\n+ && (\n+ mv variableMetadata.tsv $variableMetadata;\n+ mv dataMatrix.tsv $datamatrix;\n+ mv annotatediff.RData $rdata\n+ );\n+ cat xset.log\n+ \n+ \n+ </command>\n+\n+ <inputs>\n+ \n+ \n+ <param name="image" type="data" label="RData file" format="rdata.xcms.fillpeaks,rdata" help="output file from another function xcms (fillPeaks)" />\n+\n+ <param name="convert_param" 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"/>\n+ <param name="num_digits" type="integer" value="0" label="" help="Number of decimal places for mass values reported in ions identifiers" />\n+\n+ <param name="sigma" type="integer" value="6" label="groupFWHM: multiplier of the standard deviation" help="[sigma]" />\n+ <param name="perfwhm" type="float" value="0.6" max="1" min="0" label="groupFWHM: percentage of FWHM width" help="[perfwhm]" />\n+ <param name="maxcharge" type="integer" value="3" label="findIsotopes: max. ion charge" help="[maxcharge]" />\n+ <param name="maxiso" type="integer" value="4" label="findIsotopes: max. number of expected isotopes" help="[maxiso]" />\n+ <param name="minfrac" type="float" value="0.5" max="1" min="0" label="findIsotopes: The percentage number of samples, which must satisfy the C12/C13 rule for isotope annotation" help="[minfrac]" />\n+ <param name="ppm" type="integer" value="5" label="General ppm error" help="[ppm]" />\n+ <param name="mzabs" type="float" value="0.015" label="mzabs" help="General absolut error in m/z" />\n+ <param name="intval" type="select" label="General used intensity value" help="[intval] See the help section below">\n+ <option value="into" selected="true">into</option>\n+ <option value="maxo" >maxo</option>\n+ <option'..b' | Tabular |\n++---------------------------+---------------------------------------+------------------------------------------------+\n+|PCA |xset.annotate.dataMatrix.tsv | Tabular |\n++---------------------------+---------------------------------------+------------------------------------------------+\n+|Hierarchical Clustering |xset.annotate.dataMatrix.tsv | Tabular |\n++---------------------------+---------------------------------------+------------------------------------------------+\n+\n+\n+The output file **xset.annotate.dataMatrix.tsv** is an tabular file. You can continue your analysis using it in the following tools:\n+\n+ | Determine Vdk or Lowess\n+ | Normalization Vdk/Lowess\n+ | Anova\n+ | PCA\n+ | Hierarchical Clustering\n+\n+\n+**General schema of the metabolomic workflow**\n+\n+.. image:: annotate_workflow.png\n+\n+-----------\n+Input files\n+-----------\n+\n++---------------------------+---------------------------+\n+| Parameter : num + label | Format |\n++===========================+===========================+\n+| 1 : RData file | rdata.xcms.fillpeaks |\n++---------------------------+---------------------------+\n+\n+\n+----------\n+Parameters\n+----------\n+\n+diffreport: Intensity values to be used for the diffreport\n+----------------------------------------------------------\n+\n+ | If **value="into"**, integrated peak intensities are used.\n+ | If **value="maxo"**, maximum peak intensities are used.\n+ | If **value="intb"**, baseline corrected integrated peak intensities are used (only available if peak detection was done by \xe2\x80\x98findPeaks.centWave\xe2\x80\x99).\n+\n+\n+\n+------------\n+Output files\n+------------\n+\n+xset.annotate.variableMetadata.tsv\n+\n+ | For each metabolite (row) :\n+ | the value of the intensity in each sample, fold, anova, mzmed, mzmin, mzmax, rtmed, rtmin, rtmax, npeaks, isotopes, adduct and pcgroup\n+\n+xset.annotate.dataMatrix.tsv\n+\n+ | A tabular file which represents for each metabolite (row), the value of the intensity in each sample (column).\n+ \n+xset.annotate.zip\n+\n+ | It contains filebase_eic, filebase_box and filebase.tsv for one conditon vs another (Anova analysis).\n+\n+xset.annotate.Rdata rdata.camera.quick or rdata.camera.positive or rdata.camera.negative\n+\n+ | Rdata file, that be used outside Galaxy in R.\n+ \n+------\n+\n+.. class:: infomark \n+\n+The output **"xset.annotate.dataMatrix.tsv"** is a tabular file. You can continue your analysis using it in the following tools of the workflow:\n+\n+ | Determine Vdk or Lowess (Data correction)\n+ | Normalization Vdk/Lowess (Data correction)\n+ | Anova (Statistical analysis)\n+ | PCA (Statistical analysis)\n+ | Hierarchical Clustering (Statistical analysis)\n+\n+ \n+---------------------------------------------------\n+\n+---------------\n+Working example\n+---------------\n+\n+Input files\n+-----------\n+\n+ | RData file -> **xset.fillPeaks.RData**\n+\n+Parameters\n+----------\n+\n+ | sortpval -> **false**\n+ | sigma -> **6 (default)**\n+ | perfwhm -> **0.6 (default)**\n+ | maxcharge -> **3 (default)**\n+ | maxiso -> **4 (default)**\n+ | minfrac -> **0.5 (default)**\n+ | ppm -> **500**\n+ | mzabs -> **0.015(default)**\n+ | Advanced options -> **hide**\n+ | Numver of condition -> Two or more conditioons\n+ | eicmax -> **200**\n+ | eicwidth -> **200 (default)**\n+\n+ \n+\n+Output files\n+------------\n+\n+**Example of an xset.annotate.dataMatrix.tsv output**\n+\n+.. image:: annotatediffreport_dataMatrix.png\n+\n+**Example of a part of xset.annotate.variableMetadata.tsv output** \n+\n+.. image:: annotatediffreport_variableMetadata.png\n+\n+ </help>\n+\n+ <citations>\n+ <citation type="doi">10.1021/ac202450g</citation>\n+ <citation type="doi">10.1093/bioinformatics/btu813</citation>\n+ </citations>\n+\n+\n+</tool>\n+ \n+ \n' |
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| diff -r 000000000000 -r e0afb8854cc4 planemo.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/planemo.sh Fri Aug 07 11:08:16 2015 -0400 |
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| @@ -0,0 +1,1 @@ +planemo shed_init -f --name=camera_annotate --owner=lecorguille --description="[W4M][GC-MS] CAMERA R Package - Preprocessing - Returns annotation results (isotope peaks, adducts and fragments)" --homepage_url="http://workflow4metabolomics.org" --long_description="Part of the W4M project: http://workflow4metabolomics.org CAMERA: http://bioconductor.org/packages/release/bioc/html/CAMERA.html Wrapper skript for automatic annotation of isotope peaks, adducts and fragments for a (grouped) xcmsSet xs. The function returns an xsAnnotate object. BEWARE: this tool don't come with its script. You will need to install the dedicated package_camara_w4m_script too" --category="Metabolomics" |
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| diff -r 000000000000 -r e0afb8854cc4 repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Fri Aug 07 11:08:16 2015 -0400 |
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| @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories> + <repository changeset_revision="4a51ab3d8ecf" name="rdata_camera_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> +</repositories> |
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| diff -r 000000000000 -r e0afb8854cc4 test-data/xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv Fri Aug 07 11:08:16 2015 -0400 |
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|
| b |
| diff -r 000000000000 -r e0afb8854cc4 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Aug 07 11:08:16 2015 -0400 |
| b |
| @@ -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="camera" version="1.22.0"> + <repository changeset_revision="4386042cb931" 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="0129dc2e0e8f" name="package_camera_w4m_script_2_1" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |
