Mercurial > repos > iuc > trinity_align_and_estimate_abundance
diff align_and_estimate_abundance.xml @ 13:6d6b72d14170 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 3b8670ad0ce9dd90d6a24429bca131362e56d17d"
author | iuc |
---|---|
date | Fri, 01 Nov 2019 08:09:49 -0400 |
parents | aed859a021c0 |
children | 56162e446004 |
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--- a/align_and_estimate_abundance.xml Wed Oct 17 12:57:01 2018 -0400 +++ b/align_and_estimate_abundance.xml Fri Nov 01 08:09:49 2019 -0400 @@ -4,9 +4,8 @@ <import>macros.xml</import> </macros> <expand macro="requirements"> - <requirement type="package" version="1.3.0">rsem</requirement> - <requirement type="package" version="1.5.1">express</requirement> - <requirement type="package" version="0.43.1">kallisto</requirement> + <requirement type="package" version="1.3.2">rsem</requirement> + <requirement type="package" version="0.46.0">kallisto</requirement> </expand> <command detect_errors="aggressive"><![CDATA[ ln -f -s '$transcripts' input.fa && @@ -40,7 +39,7 @@ --transcripts input.fa --est_method $method.est_method - #if $method.est_method == "RSEM" or $method.est_method == "eXpress": + #if $method.est_method == "RSEM": --aln_method $method.aln_method #else if $method.est_method == "salmon": --salmon_idx_type $method.salmon_idx_type @@ -124,7 +123,6 @@ <conditional name="method"> <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method"> <option value="RSEM">RSEM</option> - <option value="eXpress">eXpress</option> <option value="salmon">Salmon</option> <option value="kallisto">Kallisto</option> </param> @@ -134,12 +132,6 @@ <option value="bowtie2">Bowtie2</option> </param> </when> - <when value="eXpress"> - <param type="select" name="aln_method" argument="--aln_method" label="Alignment method"> - <option value="bowtie">Bowtie</option> - <option value="bowtie2">Bowtie2</option> - </param> - </when> <when value="salmon"> <param type="select" name="salmon_idx_type" argument="--salmon_idx_type" label="Index type"> <option value="quasi">Quasi</option> @@ -173,12 +165,6 @@ <filter>method['est_method'] == "RSEM"</filter> </data> - <data format="tabular" name="isoforms_counts_express" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/results.xprs"> - <filter>method['est_method'] == "eXpress"</filter> - </data> - <data format="tabular" name="genes_counts_express" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/results.xprs.genes"> - <filter>method['est_method'] == "eXpress"</filter> - </data> <data format="tabular" name="isoforms_counts_salmon" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/quant.sf"> <filter>method['est_method'] == "salmon"</filter> @@ -248,29 +234,6 @@ <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="eXpress"/> - <param name="aln_method" value="bowtie"/> - <param name="has_gene_map" value="yes"/> - <output name="isoforms_counts_express"> - <assert_contents> - <has_line_matching expression=".*	TRINITY_DN2_c3_g1_i1	.*" /> - <has_n_columns n="15" /> - </assert_contents> - </output> - <output name="genes_counts_express"> - <assert_contents> - <has_line_matching expression="NA	TRINITY_DN3_c0_g1.*" /> - <has_n_columns n="15" /> - </assert_contents> - </output> - </test> - <test> - <param name="paired_or_single" value="paired"/> - <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"/>