Mercurial > repos > devteam > join
diff join.xml @ 4:a10f49d9218a draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
| author | devteam |
|---|---|
| date | Thu, 22 Jun 2017 18:52:36 -0400 |
| parents | ffbd1de29c28 |
| children | 718d04143c31 |
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--- a/join.xml Wed Nov 11 12:48:58 2015 -0500 +++ b/join.xml Thu Jun 22 18:52:36 2017 -0400 @@ -1,98 +1,92 @@ <tool id="gops_join_1" name="Join" version="1.0.0"> - <description>the intervals of two datasets side-by-side</description> - <requirements> - <requirement type="package" version="0.7.1">bx-python</requirement> - <requirement type="package" version="1.0.0">galaxy-ops</requirement> - </requirements> - <command interpreter="python">gops_join.py $input1 $input2 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol} -m $min -f $fill</command> - <inputs> - <param format="interval" name="input1" type="data" help="First dataset"> - <label>Join</label> - </param> - <param format="interval" name="input2" type="data" help="Second dataset"> - <label>with</label> - </param> - <param name="min" type="integer" value="1" help="(bp)"> - <label>with min overlap</label> - </param> - <param name="fill" type="select" label="Return"> - <option value="none">Only records that are joined (INNER JOIN)</option> - <option value="right">All records of first dataset (fill null with ".")</option> - <option value="left">All records of second dataset (fill null with ".")</option> - <option value="both">All records of both datasets (fill nulls with ".")</option> - </param> - </inputs> - <outputs> - <data format="interval" name="output" metadata_source="input1" /> - </outputs> - <code file="operation_filter.py"/> - <tests> - <test> - <param name="input1" value="1.bed" /> - <param name="input2" value="2.bed" /> - <param name="min" value="1" /> - <param name="fill" value="none" /> - <output name="output" file="gops-join-none.dat" /> - </test> - <test> - <param name="input1" value="1.bed" /> - <param name="input2" value="2.bed" /> - <param name="min" value="1" /> - <param name="fill" value="right" /> - <output name="output" file="gops-join-right.dat" /> - </test> - <test> - <param name="input1" value="1.bed" /> - <param name="input2" value="2.bed" /> - <param name="min" value="1" /> - <param name="fill" value="left" /> - <output name="output" file="gops-join-left.dat" /> - </test> - <test> - <param name="input1" value="1.bed" /> - <param name="input2" value="2.bed" /> - <param name="min" value="1" /> - <param name="fill" value="both" /> - <output name="output" file="gops-join-both.dat" /> - </test> - <test> - <param name="input1" value="1.bed" /> - <param name="input2" value="2.bed" /> - <param name="min" value="500" /> - <param name="fill" value="none" /> - <output name="output" file="gops-join-none-500.dat" /> - </test> - <test> - <param name="input1" value="1.bed" /> - <param name="input2" value="2.bed" /> - <param name="min" value="100" /> - <param name="fill" value="both" /> - <output name="output" file="gops-join-both-100.dat" /> - </test> - </tests> - <help> - + <description>the intervals of two datasets side-by-side</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <code file="operation_filter.py"/> + <command><![CDATA[ +python '$__tool_directory__/gops_join.py' +'$input1' +'$input2' +'$output' +-1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} +-2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol} +-m $min +-f $fill + ]]></command> + <inputs> + <param name="input1" type="data" format="interval" label="Join" help="First dataset" /> + <param name="input2" type="data" format="interval" label="With" help="Second dataset" /> + <param name="min" type="integer" value="1" label="With min overlap" help="(bp)" /> + <param name="fill" type="select" label="Return"> + <option value="none">Only records that are joined (INNER JOIN)</option> + <option value="right">All records of first dataset (fill null with ".")</option> + <option value="left">All records of second dataset (fill null with ".")</option> + <option value="both">All records of both datasets (fill nulls with ".")</option> + </param> + </inputs> + <outputs> + <data name="output" format_source="input1" metadata_source="input1" /> + </outputs> + <tests> + <test> + <param name="input1" value="1.bed" /> + <param name="input2" value="2.bed" /> + <param name="min" value="1" /> + <param name="fill" value="none" /> + <output name="output" file="gops-join-none.dat" /> + </test> + <test> + <param name="input1" value="1.bed" /> + <param name="input2" value="2.bed" /> + <param name="min" value="1" /> + <param name="fill" value="right" /> + <output name="output" file="gops-join-right.dat" /> + </test> + <test> + <param name="input1" value="1.bed" /> + <param name="input2" value="2.bed" /> + <param name="min" value="1" /> + <param name="fill" value="left" /> + <output name="output" file="gops-join-left.dat" /> + </test> + <test> + <param name="input1" value="1.bed" /> + <param name="input2" value="2.bed" /> + <param name="min" value="1" /> + <param name="fill" value="both" /> + <output name="output" file="gops-join-both.dat" /> + </test> + <test> + <param name="input1" value="1.bed" /> + <param name="input2" value="2.bed" /> + <param name="min" value="500" /> + <param name="fill" value="none" /> + <output name="output" file="gops-join-none-500.dat" /> + </test> + <test> + <param name="input1" value="1.bed" /> + <param name="input2" value="2.bed" /> + <param name="min" value="100" /> + <param name="fill" value="both" /> + <output name="output" file="gops-join-both-100.dat" /> + </test> + </tests> + <help><![CDATA[ .. class:: infomark **TIP:** If your dataset does not appear in the pulldown menu, it means that it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns. ------ - -**Screencasts!** - -See Galaxy Interval Operation Screencasts_ (right click to open this link in another window). - -.. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations - ------ +@SCREENCASTS@ **Syntax** - **Where overlap** specifies the minimum overlap between intervals that allows them to be joined. -- **Return only records that are joined** returns only the records of the first dataset that join to a record in the second dataset. This is analogous to an INNER JOIN. -- **Return all records of first dataset (fill null with ".")** returns all intervals of the first dataset, and any intervals that do not join an interval from the second dataset are filled in with a period(.). This is analogous to a LEFT JOIN. -- **Return all records of second dataset (fill null with ".")** returns all intervals of the second dataset, and any intervals that do not join an interval from the first dataset are filled in with a period(.). **Note that this may produce an invalid interval file, since a period(.) is not a valid chrom, start, end or strand.** -- **Return all records of both datasets (fill nulls with ".")** returns all records from both datasets, and fills on either the right or left with periods. **Note that this may produce an invalid interval file, since a period(.) is not a valid chrom, start, end or strand.** +- **Return only records that are joined** returns only the records of the first dataset that join to a record in the second dataset. This is analogous to an INNER JOIN. +- **Return all records of first dataset (fill null with ".")** returns all intervals of the first dataset, and any intervals that do not join an interval from the second dataset are filled in with a period(.). This is analogous to a LEFT JOIN. +- **Return all records of second dataset (fill null with ".")** returns all intervals of the second dataset, and any intervals that do not join an interval from the first dataset are filled in with a period(.). **Note that this may produce an invalid interval file, since a period(.) is not a valid chrom, start, end or strand.** +- **Return all records of both datasets (fill nulls with ".")** returns all records from both datasets, and fills on either the right or left with periods. **Note that this may produce an invalid interval file, since a period(.) is not a valid chrom, start, end or strand.** ----- @@ -115,7 +109,5 @@ All records of both datasets: .. image:: gops_joinFullOuter.gif - - -</help> + ]]></help> </tool>