Mercurial > repos > peterjc > mira_assembler
changeset 25:56dede4f0735 draft
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira3/ commit 9526de68e38a82bb84b2d9267a8c290c6adcaa65
author | peterjc |
---|---|
date | Fri, 15 Sep 2017 10:08:39 -0400 |
parents | ad14a345f1b0 |
children | 2e7e2bc0d718 |
files | tools/mira3/README.rst tools/mira3/mira.xml |
diffstat | 2 files changed, 7 insertions(+), 7 deletions(-) [+] |
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--- a/tools/mira3/README.rst Wed Jun 07 12:33:07 2017 -0400 +++ b/tools/mira3/README.rst Fri Sep 15 10:08:39 2017 -0400 @@ -10,7 +10,7 @@ separated file for use in Galaxy). It is available from the Galaxy Tool Shed at: -http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler +http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler Automated Installation @@ -32,7 +32,7 @@ The suggested location is a new ``tools/mira3`` folder. You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool by adding the line:: - + <tool file="mira3/mira.xml" /> If you wish to run the unit tests, also move/copy the ``test-data/`` files @@ -116,7 +116,7 @@ $ planemo shed_upload --tar_only tools/mira3/ ... - $ tar -tzf shed_upload.tar.gz + $ tar -tzf shed_upload.tar.gz test-data/empty_file.dat test-data/tvc_contigs.fasta test-data/tvc_mini.fastq
--- a/tools/mira3/mira.xml Wed Jun 07 12:33:07 2017 -0400 +++ b/tools/mira3/mira.xml Fri Sep 15 10:08:39 2017 -0400 @@ -54,7 +54,7 @@ ##remove_rollover_tmps, remove_tmp_directory -OUT:rrot=1:rtd=1 -##put mira temp directory on local storage +##put mira temp directory on local storage -DI:trt=/tmp </command> @@ -141,7 +141,7 @@ </outputs> <tests> <!-- Based on the MIRA v3.4.1.1 bundled minidemo/estdemo2 which uses - strain data and miraSearchESTSNPs. Here we just assemble it. --> + strain data and miraSearchESTSNPs. Here we just assemble it. --> <test> <param name="job_method" value="denovo" /> <param name="job_type" value="est" /> @@ -150,7 +150,7 @@ <param name="condSanger|use" value="true" /> <param name="condSanger|filename" value="tvc_mini.fastq" ftype="fastq" /> <param name="condRoche|use" value="false" /> - <param name="condIllumina|use" value="false" /> + <param name="condIllumina|use" value="false" /> <param name="condIonTorrent|use" value="false" /> <output name="out_fasta" file="tvc_contigs.fasta" ftype="fasta" /> <output name="out_qual" file="empty_file.dat" compare="contains" /> @@ -188,7 +188,7 @@ http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html This wrapper is available to install into other Galaxy Instances via the Galaxy -Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler +Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler </help> <citations>