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https://github.com/galaxyproject/galaxy.git
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Matthias Bernt
2395e6579b
makes column_parameter work for all datatypes setting column_names and still fallback to try to take the first line (tab separated) fixes: https://github.com/galaxyproject/galaxy/issues/17468
73 lines
2.6 KiB
XML
73 lines
2.6 KiB
XML
<tool id="column_param" name="Column Param" version="1.0.0">
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<command><![CDATA[
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cut
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-f '$col'
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#if $input1.is_of_type('csv')
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-d','
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#end if
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'$input1' > '$output1' &&
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echo "col $col" > '$output2' &&
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echo "col_names $col_names" >> '$output2'
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]]></command>
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<inputs>
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<param name="input1" type="data" format="tabular,csv" label="Input 1" />
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<param name="col" type="data_column" data_ref="input1" label="Column to Use" />
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<param name="col_names" type="data_column" data_ref="input1" use_header_names="true" label="Column to Use" />
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</inputs>
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<outputs>
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<data name="output1" format="tabular" />
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<data name="output2" format="txt" />
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</outputs>
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<tests>
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<test>
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<param name="input1" value="2.tabular" />
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<param name="col" value="2" />
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<param name="col_names" value="2" />
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<output name="output1">
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<assert_contents>
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<has_line line="68" />
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</assert_contents>
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</output>
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<output name="output2">
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<assert_contents>
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<has_line line="col 2" />
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<has_line line="col_names 2" />
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</assert_contents>
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</output>
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</test>
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<!-- test if non tabular data also creates entries by using the default
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value (which is the 1st column, but empty if filling the options fails) -->
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<test>
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<param name="input1" value="1.bed" />
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<output name="output1">
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<assert_contents>
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<has_line line="chr1" />
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</assert_contents>
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</output>
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<output name="output2">
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<assert_contents>
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<has_line line="col 1" />
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<has_line line="col_names 1" />
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</assert_contents>
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</output>
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</test>
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<!-- test csv input -->
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<test>
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<param name="input1" value="1.csv" ftype="csv"/>
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<param name="col" value="1" />
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<param name="col_names" value="c1: Transaction_date" />
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<output name="output1">
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<assert_contents>
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<has_line line="1/2/09 6:17" />
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</assert_contents>
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</output>
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<output name="output2">
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<assert_contents>
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<has_line line="col 1" />
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<has_line line="col_names 1" />
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</assert_contents>
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</output>
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</test>
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</tests>
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</tool>
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