Mercurial > repos > takakoron > distribution_of_dna_polymorphism
changeset 4:2495b1506d06 draft
Deleted selected files
| author | takakoron |
|---|---|
| date | Mon, 04 Apr 2016 23:10:07 -0400 |
| parents | fab40d775877 |
| children | 9aa9da228b8c |
| files | Visualize_Distrubution_of_polymorphism.loc Visualize_distrubution_of_polymorphism_docker.xml |
| diffstat | 2 files changed, 0 insertions(+), 78 deletions(-) [+] |
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--- a/Visualize_Distrubution_of_polymorphism.loc Mon Apr 04 23:03:21 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,35 +0,0 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a directory of BWA indexed sequences data files. You will need -#to create these data files and then create a bwa_index.loc file -#similar to this one (store it in this directory) that points to -#the directories in which those files are stored. The bwa_index.loc -#file has this format (white space characters are TAB characters): -# -#<build> <file_base> -# -#So, for example, if you had phiX indexed stored in -#/depot/data2/galaxy/phiX/base/, -#then the bwa_index.loc entry would look like this: -# -#phiX /depot/data2/galaxy/phiX/base/phiX.fa -# -#and your /depot/data2/galaxy/phiX/base/ directory -#would contain phiX.fa.* files: -# -#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb -#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann -#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt -#...etc... -# -#Your bwa_index.loc file should include an entry per line for each -#index set you have stored. The "file" in the path does not actually -#exist, but it is the prefix for the actual index files. For example: -# -#phiX /depot/data2/galaxy/phiX/base/phiX.fa -#hg18 /depot/data2/galaxy/hg18/base/hg18.fa -Oryza sativa(IRGSPbuild5) /disk/reference/ddbj/distribution_of_polymorphism/o_sativa.build5.fa -Oryza sativa(IRGSPbuild1.0) /disk/reference/ddbj/distribution_of_polymorphism/o_sativa.build1.0.fa -Arabidopsis thaliana(TAIR10) /disk/reference/ddbj/distribution_of_polymorphism/TAIR10.fa -Zea mays B73(RefGen_v2) /disk/reference/ddbj/distribution_of_polymorphism/ZmB73.RefGen2.fa -Sorghum bicolor(phytozome_v9.0_Sbicolor_v1.4) /disk/reference/ddbj/distribution_of_polymorphism/Sorbi.Sbi1.4.fa -Sorghum bicolor(phytozome_v9.0_Sbicolor_v2.1) /disk/reference/ddbj/distribution_of_polymorphism/Sorbi.Sbi12.1.fa
--- a/Visualize_distrubution_of_polymorphism_docker.xml Mon Apr 04 23:03:21 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,43 +0,0 @@ -<tool id="Visualize_distrubution_of_polymorphism_docker" name="Visualize distribution of DNA polymorphism"> - <requirements> - <container type="docker">takakoron/distribution_of_dna_polymorphism</container> - </requirements> - <command interpreter="perl"> - - /usr/src/myapp/kick_distribution_polymorphism.pl - - '$annotation_data' - '$polymorphism' - '$output1' - - </command> - - <inputs> - <!--- input annotation data --> - <param name="annotation_data" type="select" label="Select an annotation data" help="If your annotation of interest is not listed, contact the P-GALAXY team">"> - <options from_file="Visualize_Distrubution_of_polymorphism.loc"> - <column name="value" index="1" /> - <column name="name" index="0" /> - </options> - </param> - <param name="polymorphism" type="data" label="Select DNA polymorphism file(format : samtools pileup or mpileup)" /> - </inputs> - - <outputs> - <data name="output1" format="html" /> - </outputs> - -<!--- - <help> - -.. class:: infomark -**About data** - -Distribution of chromosome is appeared in order of genome file. - - </help> ---> - -</tool> - -