Mercurial > repos > takakoron > distribution_of_dna_polymorphism
changeset 5:9aa9da228b8c draft default tip
planemo upload
| author | takakoron |
|---|---|
| date | Mon, 11 Apr 2016 10:12:18 -0400 |
| parents | 2495b1506d06 |
| children | |
| files | Visualize_Distrubution_of_polymorphism.loc.sample Visualize_distrubution_of_polymorphism_docker.xml |
| diffstat | 2 files changed, 78 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Visualize_Distrubution_of_polymorphism.loc.sample Mon Apr 11 10:12:18 2016 -0400 @@ -0,0 +1,35 @@ +#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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Visualize_distrubution_of_polymorphism_docker.xml Mon Apr 11 10:12:18 2016 -0400 @@ -0,0 +1,43 @@ +<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> + +