Mercurial > repos > iuc > trinity_align_and_estimate_abundance

comparison align_and_estimate_abundance.xml @ 5:be3607a306af draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
author iuc
date Fri, 31 Mar 2017 11:37:01 -0400
parents 515119330a55
children 04bd98a9c751
comparison
equal deleted inserted replaced
4:c1fe911d84b5 5:be3607a306af
1 <tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@.2"> 1 <tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@.0">
2 <description>on a de novo assembly of RNA-Seq data</description> 2 <description>on a de novo assembly of RNA-Seq data</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"> 6 <expand macro="requirements">
7 <requirement type="package" version="1.1.2">bowtie</requirement> 7 <requirement type="package" version="1.3.0">rsem</requirement>
8 <requirement type="package" version="2.2.6">bowtie2</requirement> 8 <requirement type="package" version="1.5.1">express</requirement>
9 <requirement type="package" version="1.2.28">rsem</requirement> 9 <!-- Cannot update to salmon 0.8.2 because in Bioconda it requires icu 58, while r-base 3.3.1 requires icu 54 -->
10 <requirement type="package" version="1.5.1">eXpress</requirement> 10 <requirement type="package" version="0.8.1">salmon</requirement>
11 <requirement type="package" version="0.6.0">salmon</requirement>
12 </expand> 11 </expand>
13 <expand macro="stdio"/> 12 <command detect_errors="aggressive"><![CDATA[
14 <command><![CDATA[ 13 ln -f -s '$transcripts' input.fa &&
15 ln -s '$transcripts' input.fa &&
16 14
17 #if $inputs.paired_or_single == "paired": 15 #if $inputs.paired_or_single == "paired":
18 #if $inputs.left_input.is_of_type('fasta'): 16 #if $inputs.left_input.is_of_type('fasta'):
19 ln -s '$inputs.left_input' paired_left.fa && 17 ln -s '$inputs.left_input' paired_left.fa &&
20 ln -s '$inputs.right_input' paired_right.fa 18 ln -s '$inputs.right_input' paired_right.fa