view multijoin.xml @ 0:631dfde45073 draft default tip

First tool-shed public version

<tool id="cshl_multijoin" name="Multi-Join" version="0.1.1">
  <description>(combine multiple files)</description>
  <command interpreter="perl">multijoin
		--key '$key_column'
		--values '$value_columns'
		--filler '$filler'
		$ignore_dups
		$output_header
		$input_header
#for $file in $files
		'$file.filename'
#end for
		&gt; '$output'
  </command>

  <inputs>
	<repeat name="files" title="file to join">
		<param name="filename" label="Add file" type="data" format="txt" />
	</repeat>

	<param name="key_column" label="Common key column" type="integer"
	   value="1" help="Usually gene-ID or other common value" />

	<param name="value_columns" label="Column with values to join" type="text"
	   value="2,3,4" help="Enter comma-separated list of columns, e.g. 3,6,8">
	    <sanitizer>
		    <valid initial="string.printable">
			    <remove value="&apos;"/>
		    </valid>
	    </sanitizer>
        </param>

	<param name="output_header" type="boolean" checked="false" truevalue="--out-header" falsevalue="" label="Add header line to the output file" help="" />

	<param name="input_header" type="boolean" checked="false" truevalue="--in-header" falsevalue="" label="Input files contain a header line (as first line)" help="" />

	<param name="ignore_dups" type="boolean" checked="false" truevalue="--ignore-dups" falsevalue="" label="Ignore duplicated keys" help="If not set, duplicated keys in the same file will cause an error." />

	<param name="filler" type="text" size="20" value="0" label="Value to put in unpaired (empty) fields">
	    <sanitizer>
		    <valid initial="string.printable">
			    <remove value="&apos;"/>
		    </valid>
	    </sanitizer>
        </param>

  </inputs>
  <outputs>
    <data name="output" format="input" metadata_source="input1" />
  </outputs>

<help>
**What it does**

This tool joins multiple tabular files based on a common key column.

-----

**Example**

To join three files, based on the 4th column, and keeping the 7th,8th,9th columns:

**First file (AAA)**::

    chr4	888449	890171	FBtr0308778	0	+	266	1527	1722
    chr4	972167	979017	FBtr0310651	0	-	3944	6428	6850
    chr4	972186	979017	FBtr0089229	0	-	3944	6428	6831
    chr4	972186	979017	FBtr0089231	0	-	3944	6428	6831
    chr4	972186	979017	FBtr0089233	0	-	3944	6428	6831
    chr4	995793	996435	FBtr0111046	0	+	7	166	642
    chr4	995793	997931	FBtr0111044	0	+	28	683	2138
    chr4	995793	997931	FBtr0111045	0	+	28	683	2138
    chr4	1034029	1047719	FBtr0089223	0	-	5293	13394	13690
    ...


**Second File (BBB)**::

    chr4	90286	134453	FBtr0309803	0	+	657	29084	44167
    chr4	251355	266499	FBtr0089116	0	+	56	1296	15144
    chr4	252050	266506	FBtr0308086	0	+	56	1296	14456
    chr4	252050	266506	FBtr0308087	0	+	56	1296	14456
    chr4	252053	266528	FBtr0300796	0	+	56	1296	14475
    chr4	252053	266528	FBtr0300800	0	+	56	1296	14475
    chr4	252055	266528	FBtr0300798	0	+	56	1296	14473
    chr4	252055	266528	FBtr0300799	0	+	56	1296	14473
    chr4	252541	266528	FBtr0300797	0	+	56	1296	13987
    ...

**Third file (CCC)**::

    chr4	972167	979017	FBtr0310651	0	-	9927	6738	6850
    chr4	972186	979017	FBtr0089229	0	-	9927	6738	6831
    chr4	972186	979017	FBtr0089231	0	-	9927	6738	6831
    chr4	972186	979017	FBtr0089233	0	-	9927	6738	6831
    chr4	995793	996435	FBtr0111046	0	+	5	304	642
    chr4	995793	997931	FBtr0111044	0	+	17	714	2138
    chr4	995793	997931	FBtr0111045	0	+	17	714	2138
    chr4	1034029	1047719	FBtr0089223	0	-	17646	13536	13690
    ...


**Joining** the files, using **key column 4**, **value columns 7,8,9** and a **header line**, will return::

    key           AAA__V7   AAA__V8   AAA__V9   BBB__V7    BBB__V8    BBB__V9    CCC__V7   CCC__V8   CCC__V9
    FBtr0089116         0         0         0        56       1296      15144          0         0         0
    FBtr0089223      5293     13394     13690         0          0          0      17646     13536     13690
    FBtr0089229      3944      6428      6831         0          0          0       9927      6738      6831
    FBtr0089231      3944      6428      6831         0          0          0       9927      6738      6831
    FBtr0089233      3944      6428      6831         0          0          0       9927      6738      6831
    FBtr0111044        28       683      2138         0          0          0         17       714      2138
    FBtr0111045        28       683      2138         0          0          0         17       714      2138
    FBtr0111046         7       166       642         0          0          0          5       304       642
    FBtr0300796         0         0         0        56       1296      14475          0         0         0
    ...


# Input files need not be sorted.

-----

*multijoin* was written by A. Gordon (gordon at cshl dot edu)

</help>
</tool>