Mercurial > repos > anmoljh > align_and_estimate_abundance
changeset 0:972c930ed278 draft
Uploaded
| author | anmoljh |
|---|---|
| date | Thu, 27 Aug 2015 12:23:47 -0400 |
| parents | |
| children | 16aaa05e7d67 |
| files | align_and_estimate_abundance.xml tool_dependencies.xml |
| diffstat | 2 files changed, 78 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align_and_estimate_abundance.xml Thu Aug 27 12:23:47 2015 -0400 @@ -0,0 +1,63 @@ +<tool id='align_and_estimate_abundance' name='Align and Estimate Abundance' version='r20140717'> + +<description> using utility align_and_estimate_abundance.pl</description> + +<requirements> + <requirement type="package" version="r20140717">trinityrnaseq</requirement> + <requirement type="package" version="0.12.7">bowtie</requirement> + <requirement type="package" version="2.1">samtools</requirement> + <requirement type="package" version="1.5.1">eXpress</requirement> +</requirements> + +<command> \$TRINITY_HOME/util/align_and_estimate_abundance.pl + --transcripts $transcripts + --est_method $est_method + --aln_method $aln_method + --prep_reference + + ## Inputs. + #if str($reads.paired_or_single) == "paired": + + --left $reads.left_input --right $reads.right_input + + #if $reads.left_input.ext == 'fa': + --seqType fa + #else: + --seqType fq + #end if + + ## Additional parameters. + #if str($reads.optional.use_options) == "yes": + + #if str($reads.optional.library_type) != "None": + --SS_lib_type $reads.optional.library_type + #end if + + + + #end if + + #else: + --single $reads.input + + #if str($reads.input.ext) == 'fa': + --seqType fa + #else: + --seqType fq + #end if + + ## Additional parameters. + #if str($reads.optional.use_option) == "yes": + + #if str($reads.additional_params.library_type) != "None": + --SS_lib_type $reads.optional.library_type + #end if + + #end if + #end if + +## direct to output +> $align_and_estimate_abundance_log 2>&1 + +</command> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Aug 27 12:23:47 2015 -0400 @@ -0,0 +1,15 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="trinityrnaseq" version="r20140717"> + <repository changeset_revision="b96cec296f1d" name="package_trinityrnaseq_r20140717" prior_installation_required="True" owner="anmoljh" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="bowtie" version="0.12.7"> + <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" prior_installation_required="True" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="samtools" version="1.2"> + <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" prior_installation_required="True" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> + <package name="eXpress" version="1.5.1"> + <repository changeset_revision="93017e8743e5" name="package_express_1_5_1" prior_installation_required="True" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>