Migration: isa2w4m

tools/isa2w4m/.gitignore

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+.*.swp
+planemo-venv
+tool_test_output.*
+dist
+*-venv
+tests/output
+.python-version
+.Rproj.user

tools/isa2w4m/.travis.yml

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+dist: bionic
+
+notifications:
+ email:
+  recipients:
+   - [email protected]
+
+script:
+    - make test
+    - make plint
+    - make ptest

tools/isa2w4m/Makefile

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+SCRIPT_NAME=isa2w4m.py
+REPOS_NAME=isa2w4m
+TOOL_XML=isa2w4m.xml
+PYVER37=3.7.13
+PYVER38=3.8.12
+PYVER39=3.9.9
+PYVER=$(PYVER38) $(PYVER39)
+PYENV:=$(shell command -v pyenv)
+ifeq (,$(PYENV))
+PYTHON=python3 -s
+else
+PYTHON=$(PYENV) exec python3 -s
+endif
+VM = isa2w4m-archlinux
+CONDA_DIR=$(HOME)/plnmconda
+export TMPDIR=$(HOME)/plnmtmp
+PLANEMO_DIR=$(HOME)/plnmws
+
+all:
+
+test: $(addprefix test,37 38 39)
+
+testvm:
+	teston -rD -f Makefile -f isa2w4m.py -f isa2w4m.xml -f requirements.txt -f tests/test-isa2w4m -f test-data -c gnumake -c pyenv -c unzip -c git -t test39 archlinux/archlinux
+
+pyver:
+ifneq (,$(PYENV))
+	for ver in $(PYVER) ; do pyenv install -s $$ver ; done
+	pyenv local $(PYVER)
+endif
+	echo "Using $$($(PYTHON) --version)."
+
+define test_on_pyver
+test$(1): export PYENV_VERSION=$$(PYVER$(1))
+test$(1): pyver requirements.txt
+	$(PYTHON) -m venv test$(1)-venv
+	. test$(1)-venv/bin/activate && test "Python $$(PYENV_VERSION)" = "$$$$(python3 --version)"
+	. test$(1)-venv/bin/activate && python3 -s -m pip install --no-cache-dir --upgrade pip
+	. test$(1)-venv/bin/activate && python3 -s -m pip install --no-cache-dir -r requirements.txt
+	. test$(1)-venv/bin/activate && python3 -s -c 'import isatools'
+	. test$(1)-venv/bin/activate && tests/test-isa2w4m
+endef
+
+$(foreach ver,37 38 39,$(eval $(call test_on_pyver,$(ver))))
+
+$(TMPDIR):
+	mkdir -p "$@"
+
+# TODO Check for presence of ~/.local/lib/python* folders before running planemo.
+define ptest_on_pyver
+planemo$(1)-venv: export PYENV_VERSION=$$(PYVER$(1))
+planemo$(1)-venv: pyver
+	$(PYTHON) -m venv $$@
+	. planemo$(1)-venv/bin/activate && test "Python $$(PYENV_VERSION)" = "$$$$(python3 --version)"
+
+planemo$(1)-venv/bin/planemo: planemo$(1)-venv
+	. planemo$(1)-venv/bin/activate && python3 -s -m pip install planemo
+
+plint$(1): planemo-venv/bin/planemo
+	. planemo$(1)-venv/bin/activate && planemo --directory $(PLANEMO_DIR)$(1) lint $(TOOL_XML)
+
+ptest$(1): planemo$(1)-venv/bin/planemo $(TMPDIR)
+	. planemo$(1)-venv/bin/activate && planemo --directory $(PLANEMO_DIR)$(1) test --conda_prefix "$(CONDA_DIR)$(1)" --conda_dependency_resolution --galaxy_python_version $(subst 3,3.,$(1)) $(TOOL_XML)
+
+pttsdiff$(1): dist/$(REPOS_NAME)/ planemo$(1)-venv/bin/planemo $(HOME)/.planemo.yml
+	@echo "Check difference with testtoolshed version."
+	. planemo$(1)-venv/bin/activate && cd $$< && planemo shed_diff --shed_target testtoolshed
+
+pttsupdate$(1): dist/$(REPOS_NAME)/ planemo$(1)-venv/bin/planemo $(HOME)/.planemo.yml
+	@echo "Push new version to testtoolshed."
+	. planemo$(1)-venv/bin/activate && cd $$< && planemo shed_update --check_diff --skip_metadata --shed_target testtoolshed
+
+ptsdiff$(1): dist/$(REPOS_NAME)/ planemo$(1)-venv/bin/planemo $(HOME)/.planemo.yml
+	@echo "Check difference with toolshed version."
+	. planemo$(1)-venv/bin/activate && cd $$< && planemo shed_diff --shed_target toolshed
+
+ptsupdate$(1): dist/$(REPOS_NAME)/ planemo$(1)-venv/bin/planemo $(HOME)/.planemo.yml
+	@echo "Push new version to toolshed."
+	. planemo$(1)-venv/bin/activate && cd $$< && planemo shed_update --check_diff --skip_metadata --shed_target toolshed
+endef
+
+$(foreach ver,37 38 39,$(eval $(call ptest_on_pyver,$(ver))))
+
+plint: plint39
+
+ptest: ptest39
+
+dist/$(REPOS_NAME)/:
+	mkdir -p $@
+	cp -Lr README.md $(SCRIPT_NAME) $(TOOL_XML) test-data $@
+
+pttsdiff: pttsdiff39
+
+ptsdiff: ptsdiff39
+
+pttsupdate: pttsupdate39
+
+ptsupdate: ptsupdate39
+
+clean:
+	$(RM) -r *-venv $(HOME)/plnm*
+	$(RM) tool_test_output.*
+	$(RM) -r dist
+	$(RM) -r tests/output
+	$(RM) .python-version
+	$(RM) -r $(TMPDIR)
+
+.PHONY: all clean test plint ptest ptesttoolshed_diff ptesttoolshed_update ptoolshed_diff ptoolshed_update

tools/isa2w4m/README.md

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+# ISA2W4M
+
+[![Build Status](https://travis-ci.org/workflow4metabolomics/isa2w4m.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/isa2w4m)
+
+Convert an ISA study into the 3 TSV files format of W4M.
+
+## Updates
+
+### 1.1.2
+
+ * Changed double quotes in single quotes inside XML Command tag.
+
+### 1.1.1
+
+ * Correct planemo test.
+ * Run tests in Travis-CI.
+

tools/isa2w4m/isa2w4m.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Makefile

tools/isa2w4m/isa2w4m.py

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+#!/usr/bin/env python3
+
+from isatools.convert import isatab2w4m
+import warnings
+
+with warnings.catch_warnings():
+    warnings.simplefilter("ignore")
+    isatab2w4m.main()

tools/isa2w4m/isa2w4m.xml

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+<!-- vi: se fdm=marker : -->
+<tool id="isa2w4m" name="ISA to W4M" version="1.1.3">
+
+	<description>Convert ISA data type into W4M format</description>
+
+	<requirements>
+		<requirement type="package" version="1.2.5">pandas</requirement>
+		<requirement type="package" version="0.12.2">isatools</requirement>
+	</requirements>
+
+	<!-- Command {{{1 -->
+
+	<command><![CDATA[
+		## @@@BEGIN_CHEETAH@@@
+
+		$__tool_directory__/isa2w4m.py
+		-i '$isa.extra_files_path'
+		-s '$w4m_sample_metadata'
+		-v '$w4m_variable_metadata'
+		-m '$w4m_data_matrix'
+
+		## Choose study to output
+		#if $study:
+			-n '$study'
+		#end if
+
+		## Choose assay to output
+		#if $assay:
+			-f '$assay'
+		#end if
+
+		## Filtering
+		#if $sample_na_filtering:
+			-S '$sample_na_filtering'
+		#end if
+		#if $variable_na_filtering:
+			-V '$variable_na_filtering'
+		#end if
+
+		## Redirect stderr to stdout otherwise Galaxy thinks the tool fails if
+		## it sees just one character on stderr.
+		2>&1
+
+		## @@@END_CHEETAH@@@
+	]]></command>
+
+	<!-- Inputs {{{1 -->
+
+	<inputs>
+		<param name="isa" label="ISA" type="data" format="isa-tab"/>
+		<param name="study" type="text" size="256" value="" help="Type here the name of the assay file you want to extract from the ISA archive. If unset, the first listed study will be used."/>
+		<param name="assay" type="text" size="256" value="" help="Type here the name of the study file you want to extract from the ISA archive. If unset, the first listed assay in the study will be used"/>
+		<param name="sample_na_filtering" type="text" label="Sample metadata columns NA filtering" help="The rows that contain NA value in the specified columns will be filtered out. Column names must be separated by commas."/>
+		<param name="variable_na_filtering" type="text" label="Variable metadata columns NA filtering" help="The rows that contain NA value in the specified columns will be filtered out. Column names must be separated by commas."/>
+	</inputs>
+
+	<!-- Outputs {{{1 -->
+
+    <outputs>
+		<data name="w4m_variable_metadata" label="${isa.name} W4M var" format="tabular"/>
+        <data name="w4m_sample_metadata" label="${isa.name} W4M samp" format="tabular"/>
+        <data name="w4m_data_matrix" label="${isa.name} W4M data" format="tabular"/>
+	</outputs>
+
+	<!-- Tests {{{1 -->
+	<tests>
+		<test>
+			<param name="isa" value="MTBLS30.zip" ftype="isa-tab"/>
+			<output name="w4m_variable_metadata" file="MTBLS30-w4m-variable-metadata.tsv"/>
+			<output name="w4m_sample_metadata" file="MTBLS30-w4m-sample-metadata.tsv"/>
+			<output name="w4m_data_matrix" file="MTBLS30-w4m-sample-variable-matrix.tsv"/>
+		</test>
+		<test>
+			<param name="isa" value="MTBLS174.zip" ftype="isa-tab"/>
+			<output name="w4m_variable_metadata" file="MTBLS174-w4m-variable-metadata.tsv"/>
+			<output name="w4m_sample_metadata" file="MTBLS174-w4m-sample-metadata.tsv"/>
+			<output name="w4m_data_matrix" file="MTBLS174-w4m-sample-variable-matrix.tsv"/>
+		</test>
+	</tests>
+
+	<!-- Help {{{1 -->
+    <help>
+<!-- @@@BEGIN_RST@@@ -->
+
+====================
+ISA to W4M converter
+====================
+
+Converts an ISA-Tab dataset into W4M 3 files format.
+
+------
+Inputs
+------
+
+ISA dataset
+===========
+
+The ISA-Tab dataset to convert to W4M format.
+
+Study to extract
+================
+
+The file name of the study to extract from the ISA dataset.
+
+Assay to extract
+================
+
+The file name of the assay to extract from the ISA dataset chosen study.
+
+Sample NA filtering
+===================
+
+This is a comma separated list of column names from the sample metadata dataset.
+Rows containg NA values in one or more of the listed columns will be removed from the dataset.
+
+Variable NA filtering
+=====================
+
+This is a comma separated list of column names from the variable metadata dataset.
+Rows containg NA values in one or more of the listed columns will be removed from the dataset.
+
+-------
+Outputs
+-------
+
+The output is a set of 3 datasets:
+
+ - Samples metadata.
+ - Variables metadata.
+ - Samples x variables matrix. 
+
+<!-- @@@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>

tools/isa2w4m/requirements.txt

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+markupsafe==2.0.1
+toml>=0.9.4
+isatools==0.12.2
+planemo