add travis and git files

workflow4metabolomics · May 20, 2019 · 024b2c9 · 024b2c9
1 parent e9f7761
commit 024b2c9
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diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,2 @@
+tool_test_output.html
+tool_test_output.json
diff --git a/.travis.yml b/.travis.yml
@@ -5,19 +5,21 @@
 # See http://travis-ci.org/ for details
 language: python
 
-before_install:
- - export WRAPPER_REPO="galaxy/metaMS"
- - export GALAXY_RELEASE="release_17.01"
- - export PLANEMO_RELEASE="0.37.0"
+env:
+  - TESTFOLDER=tools/metaMS_runGC
+  - TESTFOLDER=tools/metaMS_plot
 
-install:
+before_install:
  - sudo apt-get install -y python-virtualenv
  - virtualenv planemo-venv
  - . planemo-venv/bin/activate
- - pip install --upgrade pip setuptools
- - pip install planemo==$PLANEMO_RELEASE
+ - pip install planemo==0.58.1
 
+# @TODO: remove ASAP
+# The issue: https://github.com/galaxyproject/planemo/issues/865
+install:
+  - for LINK in $(find ${TRAVIS_BUILD_DIR}/${TESTFOLDER}/test-data/ -type l -exec ls {} \;); do REALPATH=$(readlink -f $LINK); rm -f $LINK; cp $REALPATH $LINK; done
 script:
- - planemo lint "${TRAVIS_BUILD_DIR}/${WRAPPER_REPO}"
- - planemo test --conda_auto_init --conda_auto_install --conda_dependency_resolution --galaxy_branch "$GALAXY_RELEASE" --no_cache_galaxy "${TRAVIS_BUILD_DIR}/${WRAPPER_REPO}"
+ - planemo lint "${TRAVIS_BUILD_DIR}/${TESTFOLDER}"
+ - planemo test --galaxy_branch release_18.05 --no_cache_galaxy "${TRAVIS_BUILD_DIR}/${TESTFOLDER}"
 
diff --git a/tools/macro/macros.xml b/tools/macro/macros.xml
@@ -0,0 +1,77 @@
+<?xml version="1.0"?>
+
+<macros>
+
+	<xml name="stdio">
+        <stdio>
+            <exit_code range="1" level="fatal" />
+        </stdio>
+	</xml>
+
+	<xml name="requirements">
+    	<requirements>
+        	<requirement type="package" version="1.18.1">bioconductor-metams</requirement>
+        	<requirement type="package" version="1.1_4">r-batch</requirement>
+    	</requirements>   
+	</xml>
+
+	<xml name="input_file_load">
+        <section name="file_load_section" title="Resubmit your raw dataset or your zip file">
+            <conditional name="file_load_conditional">
+                <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message saying that your original dataset or zip file have been deleted on the server." >
+                    <option value="no" >no need</option>
+                    <option value="yes" >yes</option>
+                </param>
+                <when value="no">
+                </when>
+                <when value="yes">
+                    <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" multiple="true" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." />
+                </when>
+            </conditional>
+        </section>
+	</xml>
+
+	<!--<xml name="test_file_load_alg">
+        <section name="file_load_section">
+            <conditional name="file_load_conditional">
+                <param name="file_load_select" value="yes" />
+                <param name="input" value="RawFilesTest_alg2_t.mzData,RawFilesTest_alg3_t.mzData,RawFilesTest_alg7_t.mzData,RawFilesTest_alg8_t.mzData,RawFilesTest_alg9_t.mzData,RawFilesTest_alg11_t.mzData" ftype="mzdata" />
+            </conditional>
+        </section>
+	</xml>-->
+
+	<xml name="test_file_load_alg_symlink">
+        <section name="file_load_section">
+            <conditional name="file_load_conditional">
+                <param name="file_load_select" value="yes" />
+                <param name="input" value="RawFilesTest_alg2.mzData,RawFilesTest_alg3.mzData,RawFilesTest_alg7.mzData,RawFilesTest_alg8.mzData,RawFilesTest_alg9.mzData,RawFilesTest_alg11.mzData" ftype="mzdata" />
+            </conditional>
+        </section>
+	</xml>
+
+    <!-- COMMAND -->
+    <token name="@COMMAND_RSCRIPT@">LC_ALL=C Rscript $__tool_directory__/</token>
+
+    <token name="@COMMAND_LOG_EXIT@">
+        ;
+        return=\$?;
+        cat 'log.txt';
+        sh -c "exit \$return"
+    </token>
+
+    <!-- FILE_LOAD for planemo test -->
+    <!-- Change | for , because I use it in metaMS tool -->
+    <token name="@COMMAND_FILE_LOAD@">
+        #if $file_load_section.file_load_conditional.file_load_select == "yes":
+            #if $file_load_section.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section.file_load_conditional.input[0].is_of_type("netcdf"):
+                #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] )
+                #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] )
+
+                singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
+            #else
+                zipfile '$file_load_section.file_load_conditional.input'
+            #end if
+        #end if
+	</token>
+
+</macros>