Mercurial > repos > devteam > pgsnp2gd_snp
comparison pgSnp2gd_snp.xml @ 1:57c5ac41f22c draft default tip
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:27:32 -0400 |
| parents | d189d06d23cf |
| children |
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| 0:d189d06d23cf | 1:57c5ac41f22c |
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| 1 <tool id="pgSnp2gd_snp" name="pgSnp to gd_snp" hidden="false" version="1.0.0"> | 1 <tool id="pgSnp2gd_snp" name="pgSnp to gd_snp" hidden="false" version="1.0.0"> |
| 2 <description>Convert from pgSnp to gd_snp</description> | 2 <description>Convert from pgSnp to gd_snp</description> |
| 3 <command interpreter="perl"> | 3 <command interpreter="perl"> |
| 4 #if $snptab.tab2 == "yes" | 4 <![CDATA[ |
| 5 #if $snptab.colsOnly == "addColsOnly" #pgSnp2gd_snp.pl $input1 -tab=$snptab.input2 -name=$indName -build=${input1.metadata.dbkey} -addColsOnly -chr=${input1.metadata.chromCol} > $out_file1 | 5 #if $snptab.tab2 == "yes" |
| 6 #else #pgSnp2gd_snp.pl $input1 -tab=$snptab.input2 -name=$indName -build=${input1.metadata.dbkey} -ref=${ref} -chr=${input1.metadata.chromCol} > $out_file1 | 6 #if $snptab.needRef.colsOnly == "addColsOnly" |
| 7 #end if | 7 pgSnp2gd_snp.pl '$input1' -tab=${snptab.input2} -name=$indName -build=${input1.metadata.dbkey} -addColsOnly -chr=${input1.metadata.chromCol} > '$out_file1' |
| 8 #else #pgSnp2gd_snp.pl $input1 -name=$indName -build=${input1.metadata.dbkey} -ref=${ref} -chr=${input1.metadata.chromCol} > $out_file1 | 8 #else |
| 9 pgSnp2gd_snp.pl '$input1' -tab=${snptab.input2} -name=$indName -build=${input1.metadata.dbkey} -ref=${snptab.needRef.ref} -chr=${input1.metadata.chromCol} > '$out_file1' | |
| 9 #end if | 10 #end if |
| 10 </command> | 11 #else |
| 11 <inputs> | 12 pgSnp2gd_snp.pl '$input1' -name=$indName -build=${input1.metadata.dbkey} -ref=${snptab.ref} -chr=${input1.metadata.chromCol} > '$out_file1' |
| 12 <param format="tab" name="input1" type="data" label="pgSnp dataset" /> | 13 #end if |
| 13 <conditional name="snptab"> | 14 ]]> |
| 14 <param name="tab2" type="select" label="Append to gd_snp dataset in history"> | 15 </command> |
| 15 <option value="yes">yes</option> | 16 <inputs> |
| 16 <option value="no" selected="true">no</option> | 17 <param format="tab" name="input1" type="data" label="pgSnp dataset" /> |
| 17 </param> | 18 <conditional name="snptab"> |
| 18 <when value="yes"> | 19 <param name="tab2" type="select" label="Append to gd_snp dataset in history"> |
| 19 <param format="gd_snp" name="input2" type="data" label="gd_snp dataset" /> | 20 <option value="yes">yes</option> |
| 20 <conditional name="needRef"> | 21 <option value="no" selected="true">no</option> |
| 21 <param name="colsOnly" type="select" label="Skip new SNPs"> | 22 </param> |
| 22 <option value="no" selected="true">no</option> | 23 <when value="yes"> |
| 23 <option value="addColsOnly">yes</option> | 24 <param format="gd_snp" name="input2" type="data" label="gd_snp dataset" /> |
| 24 </param> | 25 <conditional name="needRef"> |
| 25 <when value="no"> | 26 <param name="colsOnly" type="select" label="Skip new SNPs"> |
| 26 <param name="ref" type="data_column" data_ref="input1" label="Column with reference allele" /> | 27 <option value="no" selected="true">no</option> |
| 27 </when> | 28 <option value="addColsOnly">yes</option> |
| 28 <when value="addColsOnly"> <!-- do nothing --> | 29 </param> |
| 29 </when> | 30 <when value="no"> |
| 31 <param name="ref" type="data_column" data_ref="input1" label="Column with reference allele" /> | |
| 32 </when> | |
| 33 <when value="addColsOnly" /> | |
| 34 </conditional> | |
| 35 </when> | |
| 36 <when value="no"> | |
| 37 <param name="ref" type="data_column" data_ref="input1" label="Column with reference allele" /> | |
| 38 </when> | |
| 30 </conditional> | 39 </conditional> |
| 31 </when> | 40 <param name="indName" type="text" label="Label for new individual/group" value="na" /> |
| 32 <when value="no"> | 41 </inputs> |
| 33 <param name="ref" type="data_column" data_ref="input1" label="Column with reference allele" /> | 42 <outputs> |
| 34 </when> | 43 <data format="gd_snp" name="out_file1" /> |
| 35 </conditional> | 44 </outputs> |
| 36 <param name="indName" type="text" size="20" label="Label for new individual/group" value="na" /> | 45 <tests> |
| 37 </inputs> | 46 <test> |
| 38 <outputs> | 47 <param name="input1" value="pgSnpTest.ref.txt" ftype="interval" dbkey="hg19" /> |
| 39 <data format="gd_snp" name="out_file1" /> | 48 <param name="tab2" value="no" /> |
| 40 </outputs> | 49 <param name="ref" value="8" /> |
| 41 <tests> | 50 <param name="indName" value="na" /> |
| 42 <test> | 51 <output name="output" file="pgSnp2snp_output.txt" /> |
| 43 <param name='input1' value='pgSnpTest.ref.txt' ftype='interval' /> | 52 </test> |
| 44 <param name='tab2' value='no' /> | 53 </tests> |
| 45 <param name='ref' value='8' /> | |
| 46 <param name='indName' value='na' /> | |
| 47 <output name="output" file="pgSnp2snp_output.txt" /> | |
| 48 </test> | |
| 49 </tests> | |
| 50 | 54 |
| 51 <help> | 55 <help> |
| 52 | |
| 53 **Dataset formats** | 56 **Dataset formats** |
| 54 | 57 |
| 55 The input dataset is of Galaxy datatype interval_, with the additional columns | 58 The input dataset is of Galaxy datatype interval_, with the additional columns |
| 56 required for pgSnp_ format. | 59 required for pgSnp_ format. |
| 57 Any further columns beyond those defined for pgSnp will be ignored. | 60 Any further columns beyond those defined for pgSnp will be ignored. |
| 67 **What it does** | 70 **What it does** |
| 68 | 71 |
| 69 This tool converts a pgSnp dataset to gd_snp format, either starting a new | 72 This tool converts a pgSnp dataset to gd_snp format, either starting a new |
| 70 dataset or appending to an old one. When appending, | 73 dataset or appending to an old one. When appending, |
| 71 if any new SNPs appear only in the pgSnp file they can either be skipped entirely, or | 74 if any new SNPs appear only in the pgSnp file they can either be skipped entirely, or |
| 72 backfilled with "-1" (meaning "unknown") for previous individuals/groups in the | 75 backfilled with "-1" (meaning "unknown") for previous individuals/groups in the |
| 73 input gd_snp dataset. | 76 input gd_snp dataset. |
| 74 If any new SNPs are being added (either by creating a new table or by backfilling), | 77 If any new SNPs are being added (either by creating a new table or by backfilling), |
| 75 then an extra column with the reference allele must be supplied in the pgSnp dataset, | 78 then an extra column with the reference allele must be supplied in the pgSnp dataset, |
| 76 as shown in the example below. | 79 as shown in the example below. |
| 77 | 80 |
| 90 | 93 |
| 91 chr1 1888681 T C -1 3 4 1 0.8893 | 94 chr1 1888681 T C -1 3 4 1 0.8893 |
| 92 chr1 3118325 C T -1 0 8 0 0.8796 | 95 chr1 3118325 C T -1 0 8 0 0.8796 |
| 93 chr1 3211457 A C -1 17 10 1 0.8576 | 96 chr1 3211457 A C -1 17 10 1 0.8576 |
| 94 etc. | 97 etc. |
| 95 | 98 </help> |
| 96 </help> | |
| 97 </tool> | 99 </tool> |