Mercurial > repos > jjohnson > snpeff
diff snpSift_caseControl.xml @ 8:13b6ad2ddace
SnpEffect v3.2
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Mon, 13 May 2013 12:45:07 -0500 |
| parents | ec16dae84230 |
| children | 937367efb1da |
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--- a/snpSift_caseControl.xml Thu Mar 28 12:29:45 2013 -0500 +++ b/snpSift_caseControl.xml Mon May 13 12:45:07 2013 -0500 @@ -1,37 +1,50 @@ -<tool id="snpSift_caseControl" name="SnpSift CaseControl" version="3.1"> - <description>Count samples are in 'case' and 'control' groups.</description> - <!-- - You will need to change the path to wherever your installation is. - You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) - --> - <requirements> - <requirement type="package" version="3.1">snpEff</requirement> - </requirements> - <command> - java -Xmx1G -jar \$JAVA_JAR_PATH/SnpSift.jar caseControl -q $hhCase $hhControl '$caseControStr' $input > $output - </command> - <inputs> - <param format="vcf" name="input" type="data" label="VCF input"/> - <param name="hhCase" type="select" label="Hom/Het case"> - <option value="any">Any</option> - <option value="hom">Homozygous</option> - <option value="het">Heterozygous</option> - </param> - <param name="hhControl" type="select" label="Hom/Het control"> - <option value="any">Any</option> - <option value="hom">Homozygous</option> - <option value="het">Heterozygous</option> - </param> - <param name="caseControStr" type="text" label="Case / Control column designation" size="50"> - <help> -Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral - </help> - <validator type="regex" message="must be only plus(+), minus(-), or zero(0) characters">[+-0]+</validator> - </param> - </inputs> - <outputs> - <data format="vcf" name="output" /> - </outputs> +<tool id="snpSift_caseControl" name="SnpSift CaseControl" version="3.2"> + <description>Count samples are in 'case' and 'control' groups.</description> + <!-- + You will need to change the path to wherever your installation is. + You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) + --> + <requirements> + <requirement type="package" version="3.2">snpEff</requirement> + </requirements> + <command> + java -Xmx1G -jar \$JAVA_JAR_PATH/SnpSift.jar caseControl -q + #if $name.__str__.strip() != '': + -name $name + #end if + #if $ctrl.ctrl_src == 'caseString': + '$ctrl.caseControlStr' + #else + -tfam "$ctrl.tfam" + #end if + $input > $output + </command> + <inputs> + <param format="vcf" name="input" type="data" label="VCF input"/> + <conditional name="ctrl"> + <param name="ctrl_src" type="select" label="Case Control defined in"> + <option value="caseString">Case Control String</option> + <option value="tfam">TFAM</option> + </param> + <when value="caseString"> + <param name="caseControlStr" type="text" label="Case / Control column designation" size="50"> + <help> + Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral + </help> + <validator type="regex" message="must be only plus(+), minus(-), or zero(0) characters">[+-0]+</validator> + </param> + </when> + <when value="tfam"> + <param format="tabular" name="tfam" type="data" label="PLINK TFAM file"/> + </when> + </conditional> + <param name="name" type="text" optional="true" label="name" help="name to append to the 'Cases' or 'Controls' tags"> + <validator type="regex" message="Use only valid ID characters">[_a-zA-Z0-9]+</validator> + </param> + </inputs> + <outputs> + <data format="vcf" name="output" /> + </outputs> <stdio> <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> <exit_code range="1:" level="fatal" description="Error" /> @@ -40,43 +53,44 @@ <test> <param name="input" ftype="vcf" value="test.private.01.vcf"/> - <param name="hhCase" value="any"/> - <param name="hhControl" value="any"/> - <param name="caseControStr" value="--"/> + <param name="ctrl_src" value="caseString"/> + <param name="caseControlStr" value="--"/> <output name="output"> <assert_contents> - <has_text text="CaseControl=0/0,0/2;" /> + <has_text text="Cases=0,0,0;" /> + <has_text text="Controls=0,0,0;" /> </assert_contents> </output> </test> <test> <param name="input" ftype="vcf" value="test.private.02.vcf"/> - <param name="hhCase" value="any"/> - <param name="hhControl" value="any"/> - <param name="caseControStr" value="--"/> + <param name="ctrl_src" value="caseString"/> + <param name="caseControlStr" value="--"/> <output name="output"> <assert_contents> - <has_text text="CaseControl=0/0,2/0;" /> + <has_text text="Cases=0,0,0;" /> + <has_text text="Controls=2,0,4;" /> </assert_contents> </output> </test> <test> <param name="input" ftype="vcf" value="test.private.02.vcf"/> - <param name="hhCase" value="any"/> - <param name="hhControl" value="any"/> - <param name="caseControStr" value="-+"/> + <param name="name" value=""/> + <param name="ctrl_src" value="caseString"/> + <param name="caseControlStr" value="-+"/> <output name="output"> <assert_contents> - <has_text text="CaseControl=1/0,1/0;" /> + <has_text text="Cases=1,0,2;" /> + <has_text text="Controls=1,0,2;" /> </assert_contents> </output> </test> </tests> - <help> + <help> **SnpSift CaseControl** @@ -107,5 +121,5 @@ For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#casecontrol - </help> + </help> </tool>