Mercurial > repos > devteam > pgsnp2gd_snp
changeset 1:57c5ac41f22c draft default tip
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:27:32 -0400 |
| parents | d189d06d23cf |
| children | |
| files | pgSnp2gd_snp.pl pgSnp2gd_snp.xml |
| diffstat | 2 files changed, 54 insertions(+), 52 deletions(-) [+] |
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--- a/pgSnp2gd_snp.pl Mon Jul 28 11:30:09 2014 -0400 +++ b/pgSnp2gd_snp.pl Tue Oct 13 12:27:32 2015 -0400 @@ -59,7 +59,7 @@ } if ($in =~ /.gz$/) { - open(FH, "zcat $in |") or die "Couldn't open $in, $!\n"; + open(FH, "zcat < $in |") or die "Couldn't open $in, $!\n"; }elsif ($in =~ /.bz2$/) { open(FH, "bzcat $in |") or die "Couldn't open $in, $!\n"; }else {
--- a/pgSnp2gd_snp.xml Mon Jul 28 11:30:09 2014 -0400 +++ b/pgSnp2gd_snp.xml Tue Oct 13 12:27:32 2015 -0400 @@ -1,55 +1,58 @@ <tool id="pgSnp2gd_snp" name="pgSnp to gd_snp" hidden="false" version="1.0.0"> - <description>Convert from pgSnp to gd_snp</description> - <command interpreter="perl"> - #if $snptab.tab2 == "yes" - #if $snptab.colsOnly == "addColsOnly" #pgSnp2gd_snp.pl $input1 -tab=$snptab.input2 -name=$indName -build=${input1.metadata.dbkey} -addColsOnly -chr=${input1.metadata.chromCol} > $out_file1 - #else #pgSnp2gd_snp.pl $input1 -tab=$snptab.input2 -name=$indName -build=${input1.metadata.dbkey} -ref=${ref} -chr=${input1.metadata.chromCol} > $out_file1 - #end if - #else #pgSnp2gd_snp.pl $input1 -name=$indName -build=${input1.metadata.dbkey} -ref=${ref} -chr=${input1.metadata.chromCol} > $out_file1 + <description>Convert from pgSnp to gd_snp</description> + <command interpreter="perl"> +<![CDATA[ +#if $snptab.tab2 == "yes" + #if $snptab.needRef.colsOnly == "addColsOnly" + pgSnp2gd_snp.pl '$input1' -tab=${snptab.input2} -name=$indName -build=${input1.metadata.dbkey} -addColsOnly -chr=${input1.metadata.chromCol} > '$out_file1' + #else + pgSnp2gd_snp.pl '$input1' -tab=${snptab.input2} -name=$indName -build=${input1.metadata.dbkey} -ref=${snptab.needRef.ref} -chr=${input1.metadata.chromCol} > '$out_file1' #end if - </command> - <inputs> - <param format="tab" name="input1" type="data" label="pgSnp dataset" /> - <conditional name="snptab"> - <param name="tab2" type="select" label="Append to gd_snp dataset in history"> - <option value="yes">yes</option> - <option value="no" selected="true">no</option> - </param> - <when value="yes"> - <param format="gd_snp" name="input2" type="data" label="gd_snp dataset" /> - <conditional name="needRef"> - <param name="colsOnly" type="select" label="Skip new SNPs"> - <option value="no" selected="true">no</option> - <option value="addColsOnly">yes</option> - </param> - <when value="no"> - <param name="ref" type="data_column" data_ref="input1" label="Column with reference allele" /> - </when> - <when value="addColsOnly"> <!-- do nothing --> - </when> +#else + pgSnp2gd_snp.pl '$input1' -name=$indName -build=${input1.metadata.dbkey} -ref=${snptab.ref} -chr=${input1.metadata.chromCol} > '$out_file1' +#end if +]]> + </command> + <inputs> + <param format="tab" name="input1" type="data" label="pgSnp dataset" /> + <conditional name="snptab"> + <param name="tab2" type="select" label="Append to gd_snp dataset in history"> + <option value="yes">yes</option> + <option value="no" selected="true">no</option> + </param> + <when value="yes"> + <param format="gd_snp" name="input2" type="data" label="gd_snp dataset" /> + <conditional name="needRef"> + <param name="colsOnly" type="select" label="Skip new SNPs"> + <option value="no" selected="true">no</option> + <option value="addColsOnly">yes</option> + </param> + <when value="no"> + <param name="ref" type="data_column" data_ref="input1" label="Column with reference allele" /> + </when> + <when value="addColsOnly" /> + </conditional> + </when> + <when value="no"> + <param name="ref" type="data_column" data_ref="input1" label="Column with reference allele" /> + </when> </conditional> - </when> - <when value="no"> - <param name="ref" type="data_column" data_ref="input1" label="Column with reference allele" /> - </when> - </conditional> - <param name="indName" type="text" size="20" label="Label for new individual/group" value="na" /> - </inputs> - <outputs> - <data format="gd_snp" name="out_file1" /> - </outputs> - <tests> - <test> - <param name='input1' value='pgSnpTest.ref.txt' ftype='interval' /> - <param name='tab2' value='no' /> - <param name='ref' value='8' /> - <param name='indName' value='na' /> - <output name="output" file="pgSnp2snp_output.txt" /> - </test> - </tests> + <param name="indName" type="text" label="Label for new individual/group" value="na" /> + </inputs> + <outputs> + <data format="gd_snp" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="input1" value="pgSnpTest.ref.txt" ftype="interval" dbkey="hg19" /> + <param name="tab2" value="no" /> + <param name="ref" value="8" /> + <param name="indName" value="na" /> + <output name="output" file="pgSnp2snp_output.txt" /> + </test> + </tests> - <help> - + <help> **Dataset formats** The input dataset is of Galaxy datatype interval_, with the additional columns @@ -69,7 +72,7 @@ This tool converts a pgSnp dataset to gd_snp format, either starting a new dataset or appending to an old one. When appending, if any new SNPs appear only in the pgSnp file they can either be skipped entirely, or -backfilled with "-1" (meaning "unknown") for previous individuals/groups in the +backfilled with "-1" (meaning "unknown") for previous individuals/groups in the input gd_snp dataset. If any new SNPs are being added (either by creating a new table or by backfilling), then an extra column with the reference allele must be supplied in the pgSnp dataset, @@ -92,6 +95,5 @@ chr1 3118325 C T -1 0 8 0 0.8796 chr1 3211457 A C -1 17 10 1 0.8576 etc. - -</help> + </help> </tool>