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181 lines
7.3 KiB
XML
181 lines
7.3 KiB
XML
<tool id="join1" name="Join two Datasets" version="2.0.2">
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<description>side by side on a specified field</description>
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<command interpreter="python">join.py $input1 $input2 $field1 $field2 $out_file1 $unmatched $partial --index_depth=3 --buffer=50000000 --fill_options_file=$fill_options_file</command>
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<inputs>
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<param format="tabular" name="input1" type="data" label="Join"/>
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<param name="field1" label="using column" type="data_column" data_ref="input1" />
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<param format="tabular" name="input2" type="data" label="with" />
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<param name="field2" label="and column" type="data_column" data_ref="input2" />
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<param name="unmatched" type="select" label="Keep lines of first input that do not join with second input">
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<option value="-u">Yes</option>
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<option value="" selected="true">No</option>
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</param>
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<param name="partial" type="select" label="Keep lines of first input that are incomplete">
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<option value="-p">Yes</option>
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<option value="" selected="true">No</option>
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</param>
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<conditional name="fill_empty_columns">
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<param name="fill_empty_columns_switch" type="select" label="Fill empty columns">
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<option value="no_fill" selected="True">No</option>
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<option value="fill_empty">Yes</option>
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</param>
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<when value="no_fill">
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<!-- do nothing -->
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</when>
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<when value="fill_empty">
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<param type="select" name="fill_columns_by" label="Only fill unjoined rows">
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<option value="fill_unjoined_only" selected="True">Yes</option>
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<option value="fill_all">No</option>
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</param>
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<conditional name="do_fill_empty_columns">
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<param name="column_fill_type" type="select" label="Fill Columns by">
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<option value="single_fill_value" selected="True">Single fill value</option>
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<option value="fill_value_by_column">Values by column</option>
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</param>
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<when value="single_fill_value">
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<param type="text" name="fill_value" label="Fill value" value="."/>
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</when>
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<when value="fill_value_by_column">
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<repeat name="column_fill1" title="Fill Column for Input 1">
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<param name="column_number1" label="Column" type="data_column" data_ref="input1" />
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<param type="text" name="fill_value1" value="."/>
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</repeat>
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<repeat name="column_fill2" title="Fill Column for Input 2">
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<param name="column_number2" label="Column" type="data_column" data_ref="input2" />
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<param type="text" name="fill_value2" value="."/>
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</repeat>
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</when>
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</conditional>
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</when>
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</conditional>
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</inputs>
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<configfiles>
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<configfile name="fill_options_file"><%
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import json
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%>
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#set $__fill_options = {}
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#if $fill_empty_columns['fill_empty_columns_switch'] == 'fill_empty':
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#set $__fill_options['fill_unjoined_only'] = $fill_empty_columns['fill_columns_by'].value == 'fill_unjoined_only'
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#if $fill_empty_columns['do_fill_empty_columns']['column_fill_type'] == 'single_fill_value':
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#set $__start_fill = $fill_empty_columns['do_fill_empty_columns']['fill_value'].value
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#else:
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#set $__start_fill = ""
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#end if
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#set $__fill_options['file1_columns'] = [ __start_fill for i in range( int( $input1.metadata.columns ) ) ]
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#set $__fill_options['file2_columns'] = [ __start_fill for i in range( int( $input2.metadata.columns ) ) ]
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#if $fill_empty_columns['do_fill_empty_columns']['column_fill_type'] == 'fill_value_by_column':
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#for column_fill1 in $fill_empty_columns['do_fill_empty_columns']['column_fill1']:
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#set $__fill_options['file1_columns'][ int( column_fill1['column_number1'].value ) - 1 ] = column_fill1['fill_value1'].value
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#end for
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#for column_fill2 in $fill_empty_columns['do_fill_empty_columns']['column_fill2']:
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#set $__fill_options['file2_columns'][ int( column_fill2['column_number2'].value ) - 1 ] = column_fill2['fill_value2'].value
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#end for
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#end if
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#end if
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${json.dumps( __fill_options )}
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</configfile>
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</configfiles>
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<outputs>
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<data format="input" name="out_file1" metadata_source="input1" />
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</outputs>
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<tests>
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<test>
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<param name="input1" value="1.bed"/>
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<param name="input2" value="2.bed"/>
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<param name="field1" value="2"/>
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<param name="field2" value="2"/>
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<param name="unmatched" value=""/>
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<param name="partial" value=""/>
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<param name="fill_empty_columns_switch" value="no_fill"/>
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<output name="out_file1" file="joiner_out1.bed"/>
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</test>
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<test>
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<param name="input1" value="1.bed"/>
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<param name="input2" value="2.bed"/>
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<param name="field1" value="2"/>
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<param name="field2" value="2"/>
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<param name="unmatched" value="Yes"/>
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<param name="partial" value="Yes"/>
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<param name="fill_empty_columns_switch" value="no_fill"/>
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<output name="out_file1" file="joiner_out2.bed"/>
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</test>
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<test>
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<param name="input1" value="1.bed"/>
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<param name="input2" value="2.bed"/>
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<param name="field1" value="2"/>
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<param name="field2" value="2"/>
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<param name="unmatched" value="Yes"/>
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<param name="partial" value="Yes"/>
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<param name="fill_empty_columns_switch" value="fill_empty"/>
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<param name="fill_columns_by" value="fill_all"/>
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<param name="column_fill_type" value="single_fill_value"/>
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<param name="fill_value" value="~"/>
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<output name="out_file1" file="joiner_out3.bed"/>
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</test>
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<test>
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<param name="input1" value="1.bed"/>
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<param name="input2" value="2.bed"/>
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<param name="field1" value="2"/>
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<param name="field2" value="2"/>
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<param name="unmatched" value="Yes"/>
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<param name="partial" value="Yes"/>
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<param name="fill_empty_columns_switch" value="fill_empty"/>
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<param name="fill_columns_by" value="fill_all"/>
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<param name="column_fill_type" value="fill_value_by_column"/>
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<param name="column_number1" value="6"/>
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<param name="fill_value1" value="+"/>
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<param name="column_number2" value="1"/>
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<param name="fill_value2" value="NoChrom"/>
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<output name="out_file1" file="joiner_out4.bed"/>
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</test>
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</tests>
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<help>
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.. class:: warningmark
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**This tool will attempt to reuse the metadata from your first input.** To change metadata assignments click on the "edit attributes" link of the history item generated by this tool.
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.. class:: infomark
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**TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert*
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-----
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**Syntax**
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This tool joins lines of two datasets on a common field. An empty string ("") is not a valid identifier.
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You may choose to include lines of your first input that do not join with your second input.
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- Columns are referenced with a **number**. For example, **3** refers to the 3rd column of a tab-delimited file.
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-----
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**Example**
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Dataset1::
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chr1 10 20 geneA
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chr1 50 80 geneB
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chr5 10 40 geneL
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Dataset2::
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geneA tumor-supressor
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geneB Foxp2
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geneC Gnas1
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geneE INK4a
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Joining the 4th column of Dataset1 with the 1st column of Dataset2 will yield::
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chr1 10 20 geneA geneA tumor-suppressor
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chr1 50 80 geneB geneB Foxp2
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Joining the 4th column of Dataset1 with the 1st column of Dataset2, while keeping all lines from Dataset1, will yield::
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chr1 10 20 geneA geneA tumor-suppressor
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chr1 50 80 geneB geneB Foxp2
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chr5 10 40 geneL
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</help>
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</tool>
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