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A bunch of tests for new linting logic. #638

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Feb 21, 2017
Merged

A bunch of tests for new linting logic. #638

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2 changes: 1 addition & 1 deletion requirements.txt
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Expand Up @@ -13,6 +13,6 @@ virtualenv
lxml
gxformat2>=0.1.1
ephemeris>=0.2.0
galaxy-lib>=17.5.0
galaxy-lib>=17.5.1
html5lib>=0.9999999,!=0.99999999,!=0.999999999,!=1.0b10,!=1.0b09 ; python_version == '2.7'
cwltool==1.0.20160726135535 ; python_version == '2.7'
30 changes: 30 additions & 0 deletions tests/data/tools/fail_bad_profile_1.xml
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<tool id="fail_bad_profile_1" name="fail_bad_profile_1" version="1.0" profile="16.01.">
<description>select param</description>
<command><![CDATA[
echo "$select_opt" > $output
]]></command>
<inputs>
<param name="select_opt" type="select" label="Option">
<option value="moo">Cow</option>
</param>
</inputs>
<outputs>
<data name="output" format="txt"/>
</outputs>
<tests>
<test>
<param name="select_opt" value="Hello World!" />
<output name="output">
<assert_contents>
<has_line line="Hello World!" />
</assert_contents>
</output>
</test>
</tests>
<help>
Some Awesome Help!
</help>
<citations>
<citation type="doi">10.1101/014043</citation>
</citations>
</tool>
30 changes: 30 additions & 0 deletions tests/data/tools/fail_bad_profile_2.xml
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<tool id="fail_bad_profile_2" name="fail_bad_profile_2" version="1.0" profile="04.12">
<description>select param</description>
<command><![CDATA[
echo "$select_opt" > $output
]]></command>
<inputs>
<param name="select_opt" type="select" label="Option">
<option value="moo">Cow</option>
</param>
</inputs>
<outputs>
<data name="output" format="txt"/>
</outputs>
<tests>
<test>
<param name="select_opt" value="Hello World!" />
<output name="output">
<assert_contents>
<has_line line="Hello World!" />
</assert_contents>
</output>
</test>
</tests>
<help>
Some Awesome Help!
</help>
<citations>
<citation type="doi">10.1101/014043</citation>
</citations>
</tool>
30 changes: 30 additions & 0 deletions tests/data/tools/fail_bad_profile_3.xml
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<tool id="fail_bad_profile_3" name="fail_bad_profile_3" version="1.0" profile="16.34">
<description>select param</description>
<command><![CDATA[
echo "$select_opt" > $output
]]></command>
<inputs>
<param name="select_opt" type="select" label="Option">
<option value="moo">Cow</option>
</param>
</inputs>
<outputs>
<data name="output" format="txt"/>
</outputs>
<tests>
<test>
<param name="select_opt" value="Hello World!" />
<output name="output">
<assert_contents>
<has_line line="Hello World!" />
</assert_contents>
</output>
</test>
</tests>
<help>
Some Awesome Help!
</help>
<citations>
<citation type="doi">10.1101/014043</citation>
</citations>
</tool>
31 changes: 31 additions & 0 deletions tests/data/tools/fail_data_name.xml
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<tool id="fail_data_name" name="fail_data_name" version="1.0">
<description>select param</description>
<command><![CDATA[
echo "$select_opt" > $output
]]>
</command>
<inputs>
<param name="select_opt" type="select" label="Option">
<option value="moo">Cow</option>
</param>
</inputs>
<outputs>
<data name="output" format="txt"/>
</outputs>
<tests>
<test>
<param name="select_opt" value="Hello World!" />
<output>
<assert_contents>
<has_line line="Hello World!" />
</assert_contents>
</output>
</test>
</tests>
<help>
Some Awesome Help!
</help>
<citations>
<citation type="doi">10.1101/014043</citation>
</citations>
</tool>
30 changes: 30 additions & 0 deletions tests/data/tools/fail_name_mismatch.xml
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<tool id="fail_name_mismatch" name="fail_name_mismatch" version="1.0">
<description>select param</description>
<command><![CDATA[
echo "$select_opt" > $output
]]></command>
<inputs>
<param name="select_opt" type="select" label="Option">
<option value="moo">Cow</option>
</param>
</inputs>
<outputs>
<data name="output" format="txt"/>
</outputs>
<tests>
<test>
<param name="select_opt" value="Hello World!" />
<output name="output1">
<assert_contents>
<has_line line="Hello World!" />
</assert_contents>
</output>
</test>
</tests>
<help>
Some Awesome Help!
</help>
<citations>
<citation type="doi">10.1101/014043</citation>
</citations>
</tool>
36 changes: 36 additions & 0 deletions tests/data/tools/fail_output_collection_name_mismatch.xml
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<tool id="fail_output_collection_name_mismatch" name="fail_output_collection_name_mismatch" version="1.0.0">
<command><![CDATA[
mkdir outputs; cd outputs; awk '{ print \$2 > \$1 ".tabular" }' $input1
]]></command>
<inputs>
<param name="input1" type="data" label="Input Table" help="Table to split on first column" format="tabular" />
</inputs>
<outputs>
<collection name="split_output" type="list" label="Table split on first column">
<discover_datasets pattern="__name_and_ext__" directory="outputs" />
</collection>
</outputs>
<tests>
<test>
<param name="input1" value="tinywga.fam" />
<output_collection name="split_outputx" type="list">
<element name="101">
<assert_contents>
<has_text_matching expression="^1\n2\n3\n$" />
</assert_contents>
</element>
<element name="1334">
<assert_contents>
<has_text_matching expression="^1\n10\n11\n12\n13\n2\n$" />
</assert_contents>
</element>
</output_collection>
</test>
</tests>
<help>
Some Awesome Help!
</help>
<citations>
<citation type="doi">10.1101/014043</citation>
</citations>
</tool>
36 changes: 36 additions & 0 deletions tests/data/tools/fail_output_collection_name_missing.xml
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<tool id="fail_output_collection_name_missing" name="fail_output_collection_name_missing" version="1.0.0">
<command><![CDATA[
mkdir outputs; cd outputs; awk '{ print \$2 > \$1 ".tabular" }' $input1
]]></command>
<inputs>
<param name="input1" type="data" label="Input Table" help="Table to split on first column" format="tabular" />
</inputs>
<outputs>
<collection name="split_output" type="list" label="Table split on first column">
<discover_datasets pattern="__name_and_ext__" directory="outputs" />
</collection>
</outputs>
<tests>
<test>
<param name="input1" value="tinywga.fam" />
<output_collection type="list">
<element name="101">
<assert_contents>
<has_text_matching expression="^1\n2\n3\n$" />
</assert_contents>
</element>
<element name="1334">
<assert_contents>
<has_text_matching expression="^1\n10\n11\n12\n13\n2\n$" />
</assert_contents>
</element>
</output_collection>
</test>
</tests>
<help>
Some Awesome Help!
</help>
<citations>
<citation type="doi">10.1101/014043</citation>
</citations>
</tool>
4 changes: 2 additions & 2 deletions tests/data/tools/ok_select_param.xml
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@@ -1,8 +1,8 @@
<tool id="ok_select_param" name="ok_select_param" version="1.0">
<description>select param</description>
<command>
<command><![CDATA[
echo "$select_opt" > $output
</command>
]]></command>
<inputs>
<param name="select_opt" type="select" label="Option">
<option value="moo">Cow</option>
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26 changes: 26 additions & 0 deletions tests/data/tools/ok_test_assert_command.xml
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<tool id="copy" name="Copy Dataset" version="1.0">
<description>copies a dataset</description>
<command>
cp $input $output
</command>
<inputs>
<param name="input1" type="data" format="txt" label="Concatenate Dataset"/>
</inputs>
<outputs>
<data name="output" format="txt"/>
</outputs>
<tests>
<test>
<param name="input1" value="1.bed"/>
<assert_command>
<has_text text="cp " />
</assert_command>
</test>
</tests>
<help>
Some Awesome Help!
</help>
<citations>
<citation type="doi">10.1101/014043</citation>
</citations>
</tool>
4 changes: 2 additions & 2 deletions tests/data/tools/ok_test_output_collections.xml
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@@ -1,7 +1,7 @@
<tool id="collection_split_on_column" name="collection_split_on_column" version="1.0.0">
<command>
<command><![CDATA[
mkdir outputs; cd outputs; awk '{ print \$2 > \$1 ".tabular" }' $input1
</command>
]]></command>
<inputs>
<param name="input1" type="data" label="Input Table" help="Table to split on first column" format="tabular" />
</inputs>
Expand Down