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Merge pull request #638 from jmchilton/lint_updates_2
A bunch of tests for new linting logic.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| <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" > $output | ||
| ]]></command> | ||
| <inputs> | ||
| <param name="select_opt" type="select" label="Option"> | ||
| <option value="moo">Cow</option> | ||
| </param> | ||
| </inputs> | ||
| <outputs> | ||
| <data name="output" format="txt"/> | ||
| </outputs> | ||
| <tests> | ||
| <test> | ||
| <param name="select_opt" value="Hello World!" /> | ||
| <output name="output"> | ||
| <assert_contents> | ||
| <has_line line="Hello World!" /> | ||
| </assert_contents> | ||
| </output> | ||
| </test> | ||
| </tests> | ||
| <help> | ||
| Some Awesome Help! | ||
| </help> | ||
| <citations> | ||
| <citation type="doi">10.1101/014043</citation> | ||
| </citations> | ||
| </tool> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| <tool id="fail_bad_profile_2" name="fail_bad_profile_2" version="1.0" profile="04.12"> | ||
| <description>select param</description> | ||
| <command><![CDATA[ | ||
| echo "$select_opt" > $output | ||
| ]]></command> | ||
| <inputs> | ||
| <param name="select_opt" type="select" label="Option"> | ||
| <option value="moo">Cow</option> | ||
| </param> | ||
| </inputs> | ||
| <outputs> | ||
| <data name="output" format="txt"/> | ||
| </outputs> | ||
| <tests> | ||
| <test> | ||
| <param name="select_opt" value="Hello World!" /> | ||
| <output name="output"> | ||
| <assert_contents> | ||
| <has_line line="Hello World!" /> | ||
| </assert_contents> | ||
| </output> | ||
| </test> | ||
| </tests> | ||
| <help> | ||
| Some Awesome Help! | ||
| </help> | ||
| <citations> | ||
| <citation type="doi">10.1101/014043</citation> | ||
| </citations> | ||
| </tool> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| <tool id="fail_bad_profile_3" name="fail_bad_profile_3" version="1.0" profile="16.34"> | ||
| <description>select param</description> | ||
| <command><![CDATA[ | ||
| echo "$select_opt" > $output | ||
| ]]></command> | ||
| <inputs> | ||
| <param name="select_opt" type="select" label="Option"> | ||
| <option value="moo">Cow</option> | ||
| </param> | ||
| </inputs> | ||
| <outputs> | ||
| <data name="output" format="txt"/> | ||
| </outputs> | ||
| <tests> | ||
| <test> | ||
| <param name="select_opt" value="Hello World!" /> | ||
| <output name="output"> | ||
| <assert_contents> | ||
| <has_line line="Hello World!" /> | ||
| </assert_contents> | ||
| </output> | ||
| </test> | ||
| </tests> | ||
| <help> | ||
| Some Awesome Help! | ||
| </help> | ||
| <citations> | ||
| <citation type="doi">10.1101/014043</citation> | ||
| </citations> | ||
| </tool> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,31 @@ | ||
| <tool id="fail_data_name" name="fail_data_name" version="1.0"> | ||
| <description>select param</description> | ||
| <command><![CDATA[ | ||
| echo "$select_opt" > $output | ||
| ]]> | ||
| </command> | ||
| <inputs> | ||
| <param name="select_opt" type="select" label="Option"> | ||
| <option value="moo">Cow</option> | ||
| </param> | ||
| </inputs> | ||
| <outputs> | ||
| <data name="output" format="txt"/> | ||
| </outputs> | ||
| <tests> | ||
| <test> | ||
| <param name="select_opt" value="Hello World!" /> | ||
| <output> | ||
| <assert_contents> | ||
| <has_line line="Hello World!" /> | ||
| </assert_contents> | ||
| </output> | ||
| </test> | ||
| </tests> | ||
| <help> | ||
| Some Awesome Help! | ||
| </help> | ||
| <citations> | ||
| <citation type="doi">10.1101/014043</citation> | ||
| </citations> | ||
| </tool> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| <tool id="fail_name_mismatch" name="fail_name_mismatch" version="1.0"> | ||
| <description>select param</description> | ||
| <command><![CDATA[ | ||
| echo "$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> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,36 @@ | ||
| <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> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,36 @@ | ||
| <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> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,26 @@ | ||
| <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> |
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