Mercurial > repos > eschen42 > w4mjoinpn

changeset 0:948bac693947 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit cedf2e01903099ef5f1bbe624afe4c2845d6bf23
author eschen42
date Sun, 29 Oct 2017 10:05:05 -0400
parents
children dcfaffec48c8
files LICENSE README README.md w4mjoinpn.sh w4mjoinpn.xml
diffstat 5 files changed, 342 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE	Sun Oct 29 10:05:05 2017 -0400
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2017 Hegeman Lab
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Sun Oct 29 10:05:05 2017 -0400
@@ -0,0 +1,5 @@
+This tool joins two sets of post-XCMS post-CAMERA Workflow4Metabolomics datasets
+(i.e., sampleMetadata, variableMetadata, dataMatrix),
+one gathered in negative ionization-mode and the other in positive ionization-mode.
+
+Please see https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper for details.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Sun Oct 29 10:05:05 2017 -0400
@@ -0,0 +1,33 @@
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1038289.svg)](https://doi.org/10.5281/zenodo.1038289)
+
+# w4mjoinpn_galaxy_wrapper
+
+This tool joins two sets of MS1 datasets for **exactly** the same set of samples, where one was gathered in positive 
+ionization-mode and the other in negative ionization-mode, for reasons set forth below.  
+
+Workflow4Metabolomics (W4M, Giacomoni *et al.*, 2014, http://dx.doi.org/10.1093/bioinformatics/btu813; http://workflow4metabolomics.org; 
+https://github.com/workflow4metabolomics) provides a suite of Galaxy tools for processing and analyzing metabolomics data.
+  
+W4M uses the XCMS package (Smith *et al.*, 2006 http://dx.doi.org/10.1021/ac051437y) to extract features and align 
+their retention times among multiple samples. 
+
+After peak extraction and alignment, W4M uses the CAMERA package (Kuhl *et al.*, 2012, http://dx.doi.org/10.1021/ac202450g) 
+"to postprocess XCMS feature lists and to collect all features related to a compound into a compound spectrum."
+
+Both of these steps are done using data collected in a single ionization mode (i.e., only negative or only positive)
+because it would not make sense to attempt to use CAMERA otherwise.
+
+However, multivariate analysis in general, and particularly the "False Discovery Rate" adjustment in hypothesis testing,
+would both benefit from having all variables (features), negative and positive, combined for one analysis.  It is also
+cumbersome to be forced to do an analysis twice, once for each ionization mode.
+
+This tool will fail:
+ * when the samples are not listed in exactly the same order in the negative-mode dataMatrix and the positive-mode dataMatrix
+ * when the samples are not listed in exactly the same order in the negative-mode sampleMetadata and the positive-mode sampleMetadata
+
+Otherwise
+  * the two dataMatrix files are concatenated, and the names of features identified from positive ionization-mode data
+are prefixed with "P"; negative, with "N".
+  * the two variableMetadata files are concatenated, and the names of features are prefixed in the same way.
+  * if sampleMetadata has a polarity column, its value is set to "posneg" in the output.
+    * Technically, the sampleMetadata file in the output is derived from the negative ionization-mode sampleMetadata.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/w4mjoinpn.sh	Sun Oct 29 10:05:05 2017 -0400
@@ -0,0 +1,140 @@
+#!/bin/bash
+# join positive and negative ionization-mode XCMS datasets for a common set of samples
+# summary:
+#   - parse and validate arguments (or abort)
+#   - check that the same samples are present in the same order in both the positive and negative mode data matrices (or abort)
+
+# Parse arguments
+#   ref: https://stackoverflow.com/questions/192249/how-do-i-parse-command-line-arguments-in-bash/14203146#14203146
+POSITIONAL=()
+while [[ $# -gt 0 ]]; do
+  key="$1"
+  case $key in
+    dmpos)
+      DMPOS="$2"
+      shift # past argument
+      shift # past value
+      ;;
+    dmneg)
+      DMNEG="$2"
+      shift # past argument
+      shift # past value
+      ;;
+    dmout)
+      DMOUT="$2"
+      shift # past argument
+      shift # past value
+      ;;
+    smpos)
+      SMPOS="$2"
+      shift # past argument
+      shift # past value
+      ;;
+    smneg)
+      SMNEG="$2"
+      shift # past argument
+      shift # past value
+      ;;
+    smout)
+      SMOUT="$2"
+      shift # past argument
+      shift # past value
+      ;;
+    vmpos)
+      VMPOS="$2"
+      shift # past argument
+      shift # past value
+      ;;
+    vmneg)
+      VMNEG="$2"
+      shift # past argument
+      shift # past value
+      ;;
+    vmout)
+      VMOUT="$2"
+      shift # past argument
+      shift # past value
+      ;;
+    *)    # unknown option
+      POSITIONAL+=("$1") # save it in an array for later
+      shift # past argument
+      ;;
+  esac
+done
+set -- "${POSITIONAL[@]}" # restore positional parameters
+if [[ -n $1 ]]; then
+  echo "unexpected argument $1"
+  echo "arguments supplied: $@"
+  exit 1
+fi
+
+# Validate that we got the expected args
+set -- ${DMPOS} ${DMNEG} ${DMOUT} ${SMPOS} ${SMNEG} ${SMOUT} ${VMPOS} ${VMNEG} ${VMOUT}
+if [[ ! -n $9 ]]; then
+  echo "expecting nine arguments"
+  echo "parsed arguments: $@"
+  exit 1
+fi
+
+# Show them what we got
+echo "dataMatrix       positive_mode ${DMPOS}"
+echo "dataMatrix       negative_mode ${DMNEG}"
+echo "dataMatrix       joined_modes  ${DMOUT}"
+echo "sampleMetadata   positive_mode ${SMPOS}"
+echo "sampleMetadata   negative_mode ${SMNEG}"
+echo "sampleMetadata   joined_modes  ${SMOUT}"
+echo "variableMetadata positive_mode ${VMPOS}"
+echo "variableMetadata negative_mode ${VMNEG}"
+echo "variableMetadata joined_modes  ${VMOUT}"
+
+# Check that sample names are the same, in the same order, for the dataMatrix in both datasets
+if [ "$( head -n 1 ${DMPOS} )" != "$( head -n 1 ${DMNEG} )" ]; then echo sample names in dataMatrix files differ;     exit 1; fi
+# Check that sample names are the same, in the same order, for the sampleMetadata in both datasets
+if [ "$( cut  -f 1 ${SMPOS} )" != "$( cut  -f 1 ${SMNEG} )" ]; then echo sample names in sampleMetadata files differ; exit 1; fi
+
+# Concatenate variableMetadata datasets to respective output file
+cat  <( head -n 1 ${VMNEG} )   <( sed -n -e '1 d; s/^/N/; p;' ${VMNEG} )  <( sed -n -e '1 d; s/^/P/; p;' ${VMPOS} ) > ${VMOUT}
+
+# Concatenate dataMatrix datasets to respective output file
+cat  <( head -n 1 ${DMNEG} )   <( sed -n -e '1 d; s/^/N/; p;' ${DMNEG} )  <( sed -n -e '1 d; s/^/P/; p;' ${DMPOS} ) > ${DMOUT}
+
+# Determine whether negative ionization-mode sampleMetadata file's column three is titled "polarity"
+
+# find the ordinal number of the first column named "polarity" of the negative ionization-mode sampleMetadata file, if any
+set -- `head -n 1 ${SMNEG}`
+POLARITY=0
+MAXCOUNT=0
+while [[ $# -gt 0 ]]; do
+  MAXCOUNT=$(( MAXCOUNT + 1 ))
+  key="$1"
+  case $key in
+    polarity)
+      if [ $POLARITY -eq 0 ]; then POLARITY=${MAXCOUNT}; fi
+      shift # past argument
+      ;;
+    *)    # unknown option
+      shift # past argument
+      ;;
+  esac
+done
+echo "Polarity is in column $POLARITY of ${SMNEG}"
+echo "There  are  $MAXCOUNT columns  in  ${SMNEG}"
+
+# Copy sampleMetadata from negative ionization-mode to output file, replacing polarity if possible
+if [ ${POLARITY} -gt 1 ]; then
+  COLBEFORE=$(( POLARITY - 1 ))
+  COLAFTER=$(( POLARITY + 1 ))
+  # Replace all entries in column three of negative ionization-mode sampleMetadata file with "posneg" in respective output file
+  if [ ${POLARITY} -lt ${MAXCOUNT} ]; then
+    # Handle the case where polarity is not in the last column
+    paste <( cut -f 1-${COLBEFORE} ${SMNEG} ) <( cut -f ${POLARITY} ${SMNEG} | sed -n -e '2,$ s/.*/posneg/; p;' )  <( cut -f ${COLAFTER}- ${SMNEG} )  > ${SMOUT}
+  else
+    # Handle the case where polarity is in the last column
+    paste <( cut -f 1-${COLBEFORE} ${SMNEG} ) <( cut -f ${POLARITY} ${SMNEG} | sed -n -e '2,$ s/.*/posneg/; p;' )  > ${SMOUT}
+  fi
+else
+  # Handle the case where polarity was not found: Copy negative ionization-mode sampleMetadata file to the respective output file
+  cp ${SMNEG} ${SMOUT}
+fi
+
+exit 0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/w4mjoinpn.xml	Sun Oct 29 10:05:05 2017 -0400
@@ -0,0 +1,143 @@
+<tool id="w4mjoinpn" name="Join +/- Ions" version="0.98.1">
+  <description>Join positive and negative ionization-mode W4M datasets for the same samples</description>
+  <requirements>
+     <requirement type="package" version="8.25">coreutils</requirement>
+     <requirement type="package" version="4.2.3.dev0">sed</requirement>
+  </requirements>
+  <stdio>
+      <exit_code range="1:" level="fatal" />
+  </stdio>
+  <command><![CDATA[
+      echo "These are the the paths to the tools used by this script:" 1>&2 ;
+      which cut sed head paste cat cp bash test 1>&2 ;
+      $__tool_directory__/w4mjoinpn.sh
+        dmneg $dmneg 
+        dmpos $dmpos 
+        dmout $dmout 
+        smneg $smneg 
+        smpos $smpos 
+        smout $smout 
+        vmneg $vmneg 
+        vmpos $vmpos 
+        vmout $vmout 
+  ]]></command>
+  <inputs>
+    <param name="dmpos" label="Data matrix positive" type="data" format="tabular" help="Positive ionization-mode: Features x samples (tabular data - decimal: '.'; missing: NA; mode: numerical; separator: tab character)" />
+    <param name="smpos" label="Sample metadata positive" type="data" format="tabular" help="Positive ionization-mode: Samples x metadata (tabular data - decimal: '.'; missing: NA; mode: character or numerical; separator: tab character)" />
+    <param name="vmpos" label="Variable metadata positive" type="data" format="tabular" help="Positive ionization-mode: Features x metadata (tabular data - decimal: '.'; missing: NA; mode: character or numerical; separator: tab character)" />
+    <param name="dmneg" label="Data matrix negative" type="data" format="tabular" help="Negative ionization-mode: Features x samples (tabular data - decimal: '.'; missing: NA; mode: numerical; separator: tab character)" />
+    <param name="smneg" label="Sample metadata negative" type="data" format="tabular" help="Negative ionization-mode: Samples x metadata (tabular data - decimal: '.'; missing: NA; mode: character or numerical; separator: tab character)" />
+    <param name="vmneg" label="Variable metadata negative" type="data" format="tabular" help="Negative ionization-mode: Features x metadata (tabular data - decimal: '.'; missing: NA; mode: character or numerical; separator: tab character)" />
+  </inputs>
+  <outputs>
+    <data name="dmout" label="${dmneg.name}.posneg" format="tabular" ></data>
+    <data name="smout" label="${smneg.name}.posneg" format="tabular" ></data>
+    <data name="vmout" label="${vmneg.name}.posneg" format="tabular" ></data>
+  </outputs>
+  <help><![CDATA[
+**Join positive and negative ionization-mode W4M datasets for the same samples**
+--------------------------------------------------------------------------------
+
+**Author** - Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu)
+
+
+Motivation
+----------
+
+Workflow4Metabolomics (W4M, Giacomoni *et al.*, 2014; http://workflow4metabolomics.org; https://github.com/workflow4metabolomics) 
+provides a suite of Galaxy tools for processing and analyzing metabolomics data.
+  
+W4M uses the XCMS package (Smith *et al.*, 2006) to extract features and align 
+their retention times among multiple samples. 
+
+After peak extraction and alignment, W4M uses the CAMERA package (Kuhl *et al.*, 2012) 
+"to postprocess XCMS feature lists and to collect all features related to a compound into a compound spectrum."
+
+Both of these steps are done using data collected in a single ionization mode (i.e., only negative or only positive)
+because it would not make sense to attempt to use CAMERA otherwise.
+
+However, performing and interpreting statistical analysis would be more convenient and statistically powerful 
+with all variables (features), negative and positive, combined for one analysis.
+
+
+Description
+-----------
+
+This tool joins two sets of MS1 datasets for **exactly** the same set of samples, where one was gathered in positive ionization
+mode and the other in negative ionization-mode, for reasons set forth above.  These datasets must be post-XCMS and post-CAMERA.
+
+This tool will fail:
+
+* when the samples are not listed in exactly the same order in the negative-mode dataMatrix and the positive-mode dataMatrix
+* when the samples are not listed in exactly the same order in the negative-mode sampleMetadata and the positive-mode sampleMetadata
+
+Otherwise:
+
+* the two dataMatrix files are concatenated, and the names of features identified from positive ionization-mode data are prefixed with "P"; negative, with "N".
+* the two variableMetadata files are concatenated, and the names of features are prefixed in the same way.
+* if sampleMetadata has a polarity column, its value is set to "posneg" in the output.  (In fact, the sampleMetadata file in the output is copied from the negative ionization-mode sampleMetadata, with the polarity replaced.)
+
+Workflow Position
+-----------------
+
+* Upstream tool category: Preprocessing
+* Downstream tool categories: Normalisation, Statistical Analysis, Quality Control, Filter and Sort
+
+Working example
+---------------
+
+**Input files**
+
+  +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+
+  | Input File                                  | Download from URL                                                                                                     |
+  +=============================================+=======================================================================================================================+
+  | Data matrix, negative ionization-mode       | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/input_dataMatrix_neg.tsv       |
+  +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+
+  | Sample metadata, negative ionization-mode   | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/input_sampleMetadata_neg.tsv   |
+  +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+
+  | Variable metadata, negative ionization-mode | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/input_variableMetadata_neg.tsv |
+  +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+
+  | Data matrix, positive ionization-mode       | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/input_dataMatrix_pos.tsv       |
+  +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+
+  | Sample metadata, positive ionization-mode   | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/input_sampleMetadata_pos.tsv   |
+  +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+
+  | Variable metadata, positive ionization-mode | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/input_variableMetadata_pos.tsv |
+  +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+
+
+**Output files**
+
+  +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+
+  | Output File                                 | Download from URL                                                                                                     |
+  +=============================================+=======================================================================================================================+
+  | Data matrix                                 | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/output_dataMatrix.tsv          |
+  +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+
+  | Sample metadata                             | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/output_sampleMetadata.tsv      |
+  +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+
+  | Variable metadata                           | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/output_variableMetadata.tsv    |
+  +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+
+
+  ]]></help>
+  <citations>
+    <citation type="doi">10.5281/zenodo.1038289</citation>
+    <!--
+    <citation type="bibtex">
+      @misc{
+        w4mjoinpn_galaxy_wrapper,
+        author = {Eschenlauer, Arthur},
+        year = {2017},
+        title = {w4mjoinpn_galaxy_wrapper},
+        publisher = {GitHub},
+        journal = {GitHub repository},
+        url = {https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper},
+        doi = 10.5281/zenodo.1038290
+      }
+    </citation>
+    -->
+    <!-- Giacomoni, 2014 Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics -->
+    <citation type="doi">10.1093/bioinformatics/btu813</citation>
+    <!-- Kuhl et al., 2012 -->
+    <citation type="doi">10.1021/ac202450g</citation>
+    <!-- Smith, 2006 XCMS: Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification. -->
+    <citation type="doi">10.1021/ac051437y</citation>
+  </citations>
+</tool>