Mercurial > repos > mvdbeek > get_reference_fasta
changeset 2:d79153e68957 draft default tip
Uploaded
| author | mvdbeek |
|---|---|
| date | Tue, 28 Apr 2015 09:59:01 -0400 |
| parents | 3e37447e0b26 |
| children | |
| files | all_fasta.loc.sample get_reference_fasta.xml |
| diffstat | 2 files changed, 3 insertions(+), 21 deletions(-) [+] |
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--- a/all_fasta.loc.sample Tue Apr 28 09:44:23 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ -#This file lists the locations and dbkeys of all the fasta files -#under the "genome" directory (a directory that contains a directory -#for each build). The script extract_fasta.py will generate the file -#all_fasta.loc. This file has the format (white space characters are -#TAB characters): -# -#<unique_build_id> <dbkey> <display_name> <file_path> -# -#So, all_fasta.loc could look something like this: -# -#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa -#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa -#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa -# -#Your all_fasta.loc file should contain an entry for each individual -#fasta file. So there will be multiple fasta files for each build, -#such as with hg19 above. -#
--- a/get_reference_fasta.xml Tue Apr 28 09:44:23 2015 -0400 +++ b/get_reference_fasta.xml Tue Apr 28 09:59:01 2015 -0400 @@ -1,4 +1,4 @@ -<tool id="get_fasta_reference" name="get fasta reference" version="0.1.0"> +<tool id="get_fasta_reference" name="get fasta reference" version="0.1.1"> <description>Obtain reference genome sequence</description> <stdio> <exit_code range="1:" /> @@ -12,11 +12,11 @@ </param> </inputs> <outputs> - <data name="output" format="fasta" /> + <data name="output" label="${pre_installed_fasta.value_label}" format="fasta" /> </outputs> <tests> <test> - <param name="input" value="EcR_USP_224.fa"/> + <param name="pre_installed_fasta" value="EcR_USP_224.fa"/> <output name="output" file="EcR_USP_224.fa"/> </test> </tests>