| Previous changeset 17:6c20d62180af (2021-09-10) Next changeset 19:c2b82a94493e (2021-12-19) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c468d2b9613f88cc5f96f77ab1e0592d3c9ce707" |
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modified:
align_and_estimate_abundance.xml |
| b |
| diff -r 6c20d62180af -r 00719b8004c9 align_and_estimate_abundance.xml --- a/align_and_estimate_abundance.xml Fri Sep 10 22:42:30 2021 +0000 +++ b/align_and_estimate_abundance.xml Sat Nov 27 10:13:50 2021 +0000 |
| b |
| @@ -1,9 +1,9 @@ <tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@+galaxy1"> <description>on a de novo assembly of RNA-Seq data</description> - <expand macro="bio_tools"/> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools"/> <expand macro="requirements"> <requirement type="package" version="1.3.2">rsem</requirement> <requirement type="package" version="0.46.0">kallisto</requirement> @@ -190,11 +190,11 @@ <param name="left_input" value="reads.left.fq.gz"/> <param name="right_input" value="reads.right.fq.gz"/> <param name="transcripts" value="raw/Trinity.fasta"/> - <param name="gene_to_trans" value="raw/Trinity.map" /> <param name="library_type" value="RF"/> <param name="est_method" value="RSEM"/> <param name="aln_method" value="bowtie"/> <param name="has_gene_map" value="yes"/> + <param name="gene_trans_map" value="raw/Trinity.map" /> <output name="isoforms_counts_rsem"> <assert_contents> <has_line_matching expression="TRINITY_DN0_c0_g1_i1	.*" /> @@ -213,11 +213,11 @@ <param name="left_input" value="reads.left.fq"/> <param name="right_input" value="reads.right.fq"/> <param name="transcripts" value="raw/Trinity.fasta"/> - <param name="gene_to_trans" value="raw/Trinity.map" /> <param name="library_type" value="RF"/> <param name="est_method" value="RSEM"/> <param name="aln_method" value="bowtie2"/> <param name="has_gene_map" value="yes"/> + <param name="gene_trans_map" value="raw/Trinity.map" /> <output name="isoforms_counts_rsem"> <assert_contents> <has_line_matching expression="TRINITY_DN0_c0_g1_i1	.*" /> @@ -236,11 +236,11 @@ <param name="left_input" value="reads.left.fq"/> <param name="right_input" value="reads.right.fq"/> <param name="transcripts" value="raw/Trinity.fasta"/> - <param name="gene_to_trans" value="raw/Trinity.map" /> <param name="library_type" value="RF"/> <param name="est_method" value="salmon"/> <param name="aln_method" value="bowtie"/> <param name="has_gene_map" value="yes"/> + <param name="gene_trans_map" value="raw/Trinity.map" /> <output name="isoforms_counts_salmon"> <assert_contents> <has_line_matching expression="TRINITY_DN2_c3_g1_i1	.*" /> @@ -259,10 +259,10 @@ <param name="left_input" value="reads.left.fq"/> <param name="right_input" value="reads.right.fq"/> <param name="transcripts" value="raw/Trinity.fasta"/> - <param name="gene_to_trans" value="raw/Trinity.map" /> <param name="library_type" value="RF"/> <param name="est_method" value="kallisto"/> <param name="has_gene_map" value="yes"/> + <param name="gene_trans_map" value="raw/Trinity.map" /> <output name="isoforms_counts_kallisto"> <assert_contents> <has_line_matching expression="TRINITY_DN1_c0_g1_i1	.*" /> |