# HG changeset patch
# User prog
# Date 1578487813 18000
# Node ID 975585306dc4ca5f6dc507fab200205e68c58096
"planemo upload commit c2694fb4aa55c4f25eb53db73496eaf5e56d7872"
diff -r 000000000000 -r 975585306dc4 README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Wed Jan 08 07:50:13 2020 -0500
@@ -0,0 +1,12 @@
+# ISA extractor
+
+[](https://travis-ci.org/workflow4metabolomics/isa-extractor)
+
+Extract collections of raw data files (mzML, mzXML, netCDF, mzData or nmrML) from an ISA study.
+
+## Updates
+
+### 1.3.0
+
+ * Wrote planemo tests for all tools.
+ * Run tests in Travis-CI.
diff -r 000000000000 -r 975585306dc4 extract-from-isa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/extract-from-isa Wed Jan 08 07:50:13 2020 -0500
@@ -0,0 +1,130 @@
+#!/bin/bash
+# vi: fdm=marker
+
+# Constants {{{1
+################################################################
+
+PROG_NAME=$(basename $0)
+PROG_PATH=$(dirname $0)
+YES=yes
+NO=no
+
+# Global variables {{{1
+################################################################
+
+DEBUG=0
+EXT=
+INPUT_DIR=
+OUTPUT_DIR=
+SYMLINK=$NO
+
+# Print help {{{1
+################################################################
+
+function print_help {
+ echo "Usage: $PROG_NAME -i <ISA_DIR> -e <EXT> -o <OUTPUT_DIR>"
+ echo
+ echo "Extract files with a given extension from ISA-Tab archives into a collection."
+ echo
+ echo "Options:"
+ echo " -e, --ext EXT The extension of the files to find."
+ echo " -h, --help Print this help message."
+ echo " -i, --input DIR Input directory containing ISA archive."
+ echo " -o, --output DIR Set the output directory to use."
+ echo " -s, --symlink Create symbolic links instead of copying files."
+}
+
+# Error {{{1
+################################################################
+
+function error {
+
+ local msg=$1
+
+ echo "ERROR: $msg" >&2
+
+ exit 1
+}
+
+# Print debug msg {{{1
+################################################################
+
+function print_debug_msg {
+
+ local dbglvl=$1
+ local dbgmsg=$2
+
+ [ $DEBUG -ge $dbglvl ] && echo "[DEBUG] $dbgmsg" >&2
+}
+
+# Read args {{{1
+################################################################
+
+function read_args {
+
+ local args="$*" # save arguments for debugging purpose
+
+ # Read options
+ while true ; do
+ shift_count=1
+ case $1 in
+ -e|--ext) EXT="$2" ; shift_count=2 ;;
+ -g|--debug) DEBUG=$((DEBUG + 1)) ;;
+ -h|--help) print_help ; exit 0 ;;
+ -i|--input) INPUT_DIR="$2" ; shift_count=2 ;;
+ -o|--output) OUTPUT_DIR="$2" ; shift_count=2 ;;
+ -s|--symlink) SYMLINK=$YES ;;
+ -) error "Illegal option $1." ;;
+ --) error "Illegal option $1." ;;
+ --*) error "Illegal option $1." ;;
+ -?) error "Unknown option $1." ;;
+ -[^-]*) split_opt=$(echo $1 | sed 's/^-//' | sed 's/\([a-zA-Z]\)/ -\1/g') ; set -- $1$split_opt "${@:2}" ;;
+ *) break
+ esac
+ shift $shift_count
+ done
+ shift $((OPTIND - 1))
+
+ # Debug
+ print_debug_msg 1 "Arguments are : $args"
+
+ # Check input params
+ [[ $# -eq 0 ]] || error "No remaining arguments are allowed."
+ [[ -n $INPUT_DIR ]] || error "You must specify an input directory, using -i option."
+ [[ -d $INPUT_DIR ]] || error "\"$INPUT_DIR\" is not a valid directory."
+ [[ -n $OUTPUT_DIR ]] || error "You must specify an output directory, using -o option."
+ [[ ! -e $OUTPUT_DIR ]] || error "\"$OUTPUT_DIR\" already exists."
+ [[ -n $EXT ]] || error "You must specify the extension of the files you are looking for, with the -e option."
+}
+
+# MAIN {{{1
+################################################################
+
+read_args "$@"
+
+# Create output directory
+print_debug_msg 1 "Create output directory \"$OUTPUT_DIR\"."
+mkdir -p "$OUTPUT_DIR"
+
+# Find files to extract
+print_debug_msg 1 "Find \"$EXT\" files to extract in \"$INPUT_DIR\"."
+files_to_extract=$(mktemp -t tmp.XXXXXX)
+find "$(realpath $INPUT_DIR)" -iname "*.$EXT" >files_to_extract
+print_debug_msg 1 "Files to extract:"
+if [[ $DEBUG -ge 1 ]] ; then
+ cat files_to_extract >&2
+fi
+
+# Extract files
+if [[ $SYMLINK == $YES ]] ; then
+ print_debug_msg 1 "Create symbolic links of all \"$EXT\" files to extract into \"$OUTPUT_DIR\"."
+ xargs -I % ln -s % "$OUTPUT_DIR" <files_to_extract
+else
+ print_debug_msg 1 "Copy all \"$EXT\" files to extract to \"$OUTPUT_DIR\"."
+ xargs -I % cp % "$OUTPUT_DIR" <files_to_extract
+fi
+rm files_to_extract
+print_debug_msg 1 "Files extracted:"
+if [[ $DEBUG -ge 1 ]] ; then
+ ls -1 "$OUTPUT_DIR" >&2
+fi
diff -r 000000000000 -r 975585306dc4 isa2mzdata.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/isa2mzdata.xml Wed Jan 08 07:50:13 2020 -0500
@@ -0,0 +1,77 @@
+<!-- vi: se fdm=marker : -->
+<tool id="isa2mzdata" name="ISA to mzData" version="1.3.0">
+
+ <description>Extract mzData files from an ISA dataset and output a collection of mzData dataset.</description>
+
+ <!-- Command {{{1 -->
+
+ <command><![CDATA[
+ ## @@@BEGIN_CHEETAH@@@
+
+ $__tool_directory__/extract-from-isa
+ -i "$isa.extra_files_path"
+ -e mzData
+ -o mzData
+
+ ## @@@END_CHEETAH@@@
+ ]]></command>
+
+ <!-- Inputs {{{1 -->
+
+ <inputs>
+ <param name="isa" label="ISA" type="data" format="isa-tab"/>
+ </inputs>
+
+ <!-- Outputs {{{1 -->
+
+ <outputs>
+ <collection name="mzData" type="list" label="mzData files">
+ <discover_datasets pattern="(?P<designation>.+)\.[mM][zZ][dD][aA][tT][aA]$" directory="mzData" format="mzdata"/>
+ </collection>
+ </outputs>
+
+ <!-- Tests {{{1 -->
+ <tests>
+ <test>
+ <param name="isa" value="mzdata_study.zip" ftype="isa-tab"/>
+ <output_collection name="mzData" type="list" count="1">
+ <element name="empty" file="mzdata_study_output/empty.mzData" ftype="mzdata"/>
+ </output_collection>
+ </test>
+ </tests>
+
+ <!-- Help {{{1 -->
+ <help>
+<!-- @@@BEGIN_RST@@@ -->
+
+====================
+ISA to mzData
+====================
+
+Extract mzData files contained inside an ISA archive.
+
+-----
+Input
+-----
+
+ISA dataset
+===========
+
+The ISA-Tab dataset from which to extract the files.
+
+------
+Output
+------
+
+The output is a collection of mzData files.
+
+<!-- @@@END_RST@@@ -->
+ </help>
+
+ <!-- Citations {{{1 -->
+ <citations>
+ <citation type="doi">10.1038/ng.1054</citation> <!-- ISA -->
+ <citation type="doi">10.1093/bioinformatics/btu813</citation> <!-- W4M -->
+ </citations>
+
+</tool>
diff -r 000000000000 -r 975585306dc4 isa2mzml.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/isa2mzml.xml Wed Jan 08 07:50:13 2020 -0500
@@ -0,0 +1,77 @@
+<!-- vi: se fdm=marker : -->
+<tool id="isa2mzml" name="ISA to mzML" version="1.3.0">
+
+ <description>Extract mzML files from an ISA dataset and output a collection of mzML dataset.</description>
+
+ <!-- Command {{{1 -->
+
+ <command><![CDATA[
+ ## @@@BEGIN_CHEETAH@@@
+
+ $__tool_directory__/extract-from-isa
+ -i "$isa.extra_files_path"
+ -e mzML
+ -o mzML
+
+ ## @@@END_CHEETAH@@@
+ ]]></command>
+
+ <!-- Inputs {{{1 -->
+
+ <inputs>
+ <param name="isa" label="ISA" type="data" format="isa-tab"/>
+ </inputs>
+
+ <!-- Outputs {{{1 -->
+
+ <outputs>
+ <collection name="mzML" type="list" label="mzML files">
+ <discover_datasets pattern="(?P<designation>.+)\.[mM][zZ][mM][lL]$" directory="mzML" format="mzml"/>
+ </collection>
+ </outputs>
+
+ <!-- Tests {{{1 -->
+ <tests>
+ <test>
+ <param name="isa" value="mzml_study.zip" ftype="isa-tab"/>
+ <output_collection name="mzML" type="list" count="1">
+ <element name="empty" file="mzml_study_output/empty.mzML" ftype="mzml"/>
+ </output_collection>
+ </test>
+ </tests>
+
+ <!-- Help {{{1 -->
+ <help>
+<!-- @@@BEGIN_RST@@@ -->
+
+====================
+ISA to mzML
+====================
+
+Extract mzML files contained inside an ISA archive.
+
+-----
+Input
+-----
+
+ISA dataset
+===========
+
+The ISA-Tab dataset from which to extract the files.
+
+------
+Output
+------
+
+The output is a collection of mzML files.
+
+<!-- @@@END_RST@@@ -->
+ </help>
+
+ <!-- Citations {{{1 -->
+ <citations>
+ <citation type="doi">10.1038/ng.1054</citation> <!-- ISA -->
+ <citation type="doi">10.1093/bioinformatics/btu813</citation> <!-- W4M -->
+ </citations>
+
+</tool>
diff -r 000000000000 -r 975585306dc4 isa2mzxml.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/isa2mzxml.xml Wed Jan 08 07:50:13 2020 -0500
@@ -0,0 +1,77 @@
+<!-- vi: se fdm=marker : -->
+<tool id="isa2mzxml" name="ISA to mzXML" version="1.3.0">
+
+ <description>Extract mzXML files from an ISA dataset and output a collection of mzXML dataset.</description>
+
+ <!-- Command {{{1 -->
+
+ <command><![CDATA[
+ ## @@@BEGIN_CHEETAH@@@
+
+ $__tool_directory__/extract-from-isa
+ -i "$isa.extra_files_path"
+ -e mzXML
+ -o mzXML
+
+ ## @@@END_CHEETAH@@@
+ ]]></command>
+
+ <!-- Inputs {{{1 -->
+
+ <inputs>
+ <param name="isa" label="ISA" type="data" format="isa-tab"/>
+ </inputs>
+
+ <!-- Outputs {{{1 -->
+
+ <outputs>
+ <collection name="mzXML" type="list" label="mzXML files">
+ <discover_datasets pattern="(?P<designation>.+)\.[mM][zZ][xX][mM][lL]$" directory="mzXML" format="mzxml"/>
+ </collection>
+ </outputs>
+
+ <!-- Tests {{{1 -->
+ <tests>
+ <test>
+ <param name="isa" value="mzxml_study.zip" ftype="isa-tab"/>
+ <output_collection name="mzXML" type="list" count="1">
+ <element name="empty" file="mzxml_study_output/empty.mzXML" ftype="mzxml"/>
+ </output_collection>
+ </test>
+ </tests>
+
+ <!-- Help {{{1 -->
+ <help>
+<!-- @@@BEGIN_RST@@@ -->
+
+====================
+ISA to mzXML
+====================
+
+Extract mzXML files contained inside an ISA archive.
+
+-----
+Input
+-----
+
+ISA dataset
+===========
+
+The ISA-Tab dataset from which to extract the files.
+
+------
+Output
+------
+
+The output is a collection of mzXML files.
+
+<!-- @@@END_RST@@@ -->
+ </help>
+
+ <!-- Citations {{{1 -->
+ <citations>
+ <citation type="doi">10.1038/ng.1054</citation> <!-- ISA -->
+ <citation type="doi">10.1093/bioinformatics/btu813</citation> <!-- W4M -->
+ </citations>
+
+</tool>
diff -r 000000000000 -r 975585306dc4 isa2netcdf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/isa2netcdf.xml Wed Jan 08 07:50:13 2020 -0500
@@ -0,0 +1,77 @@
+<!-- vi: se fdm=marker : -->
+<tool id="isa2netcdf" name="ISA to netCDF" version="1.3.0">
+
+ <description>Extract netCDF files from an ISA dataset and output a collection of netCDF dataset.</description>
+
+ <!-- Command {{{1 -->
+
+ <command><![CDATA[
+ ## @@@BEGIN_CHEETAH@@@
+
+ $__tool_directory__/extract-from-isa
+ -i "$isa.extra_files_path"
+ -e CDF
+ -o netCDF
+
+ ## @@@END_CHEETAH@@@
+ ]]></command>
+
+ <!-- Inputs {{{1 -->
+
+ <inputs>
+ <param name="isa" label="ISA" type="data" format="isa-tab"/>
+ </inputs>
+
+ <!-- Outputs {{{1 -->
+
+ <outputs>
+ <collection name="netCDF" type="list" label="netCDF files">
+ <discover_datasets pattern="(?P<designation>.+)\.[cC][dD][fF]$" directory="netCDF" format="netcdf"/>
+ </collection>
+ </outputs>
+
+ <!-- Tests {{{1 -->
+ <tests>
+ <test>
+ <param name="isa" value="netcdf_study.zip" ftype="isa-tab"/>
+ <output_collection name="netCDF" type="list" count="1">
+ <element name="empty" file="netcdf_study_output/empty.CDF" ftype="netcdf"/>
+ </output_collection>
+ </test>
+ </tests>
+
+ <!-- Help {{{1 -->
+ <help>
+<!-- @@@BEGIN_RST@@@ -->
+
+====================
+ISA to netCDF
+====================
+
+Extract netCDF files contained inside an ISA archive.
+
+-----
+Input
+-----
+
+ISA dataset
+===========
+
+The ISA-Tab dataset from which to extract the files.
+
+------
+Output
+------
+
+The output is a collection of netCDF files.
+
+<!-- @@@END_RST@@@ -->
+ </help>
+
+ <!-- Citations {{{1 -->
+ <citations>
+ <citation type="doi">10.1038/ng.1054</citation> <!-- ISA -->
+ <citation type="doi">10.1093/bioinformatics/btu813</citation> <!-- W4M -->
+ </citations>
+
+</tool>
diff -r 000000000000 -r 975585306dc4 isa2nmrml.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/isa2nmrml.xml Wed Jan 08 07:50:13 2020 -0500
@@ -0,0 +1,77 @@
+<!-- vi: se fdm=marker : -->
+<tool id="isa2nmrml" name="ISA to nmrML" version="1.3.0">
+
+ <description>Extract nmrML files from an ISA dataset and output a collection of nmrML dataset.</description>
+
+ <!-- Command {{{1 -->
+
+ <command><![CDATA[
+ ## @@@BEGIN_CHEETAH@@@
+
+ $__tool_directory__/extract-from-isa
+ -i "$isa.extra_files_path"
+ -e nmrML
+ -o nmrML
+
+ ## @@@END_CHEETAH@@@
+ ]]></command>
+
+ <!-- Inputs {{{1 -->
+
+ <inputs>
+ <param name="isa" label="ISA" type="data" format="isa-tab"/>
+ </inputs>
+
+ <!-- Outputs {{{1 -->
+
+ <outputs>
+ <collection name="nmrML" type="list" label="nmrML files">
+ <discover_datasets pattern="(?P<designation>.+)\.[nN][mM][rR][mM][lL]$" directory="nmrML" format="nmrml"/>
+ </collection>
+ </outputs>
+
+ <!-- Tests {{{1 -->
+ <tests>
+ <test>
+ <param name="isa" value="nmrml_study.zip" ftype="isa-tab"/>
+ <output_collection name="nmrML" type="list" count="1">
+ <element name="empty" file="nmrml_study_output/empty.nmrML" ftype="nmrml"/>
+ </output_collection>
+ </test>
+ </tests>
+
+ <!-- Help {{{1 -->
+ <help>
+<!-- @@@BEGIN_RST@@@ -->
+
+====================
+ISA to nmrML
+====================
+
+Extract nmrML files contained inside an ISA archive.
+
+-----
+Input
+-----
+
+ISA dataset
+===========
+
+The ISA-Tab dataset from which to extract the files.
+
+------
+Output
+------
+
+The output is a collection of nmrML files.
+
+<!-- @@@END_RST@@@ -->
+ </help>
+
+ <!-- Citations {{{1 -->
+ <citations>
+ <citation type="doi">10.1038/ng.1054</citation> <!-- ISA -->
+ <citation type="doi">10.1093/bioinformatics/btu813</citation> <!-- W4M -->
+ </citations>
+
+</tool>
diff -r 000000000000 -r 975585306dc4 test-data/mzdata_study.zip
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diff -r 000000000000 -r 975585306dc4 test-data/mzdata_study_output/empty.mzData
diff -r 000000000000 -r 975585306dc4 test-data/mzml_study.zip
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diff -r 000000000000 -r 975585306dc4 test-data/mzml_study_output/empty.mzML
diff -r 000000000000 -r 975585306dc4 test-data/mzxml_study.zip
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diff -r 000000000000 -r 975585306dc4 test-data/mzxml_study_output/empty.mzXML
diff -r 000000000000 -r 975585306dc4 test-data/netcdf_study.zip
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diff -r 000000000000 -r 975585306dc4 test-data/netcdf_study_output/empty.CDF
diff -r 000000000000 -r 975585306dc4 test-data/nmrml_study.zip
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diff -r 000000000000 -r 975585306dc4 test-data/nmrml_study_output/empty.nmrML