Mercurial > repos > iuc > trinity_align_and_estimate_abundance
changeset 6:04bd98a9c751 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
| author | iuc |
|---|---|
| date | Mon, 28 Aug 2017 16:54:12 -0400 |
| parents | be3607a306af |
| children | 3baf18bcf03e |
| files | align_and_estimate_abundance.xml test-data/count/kallisto/abundance.tsv test-data/count/kallisto/abundance.tsv.genes test-data/count/kallisto/abundance_B.tsv test-data/count/kallisto/abundance_B.tsv.genes |
| diffstat | 5 files changed, 67 insertions(+), 4 deletions(-) [+] |
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--- a/align_and_estimate_abundance.xml Fri Mar 31 11:37:01 2017 -0400 +++ b/align_and_estimate_abundance.xml Mon Aug 28 16:54:12 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@.0"> +<tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@.2"> <description>on a de novo assembly of RNA-Seq data</description> <macros> <import>macros.xml</import> @@ -8,6 +8,7 @@ <requirement type="package" version="1.5.1">express</requirement> <!-- Cannot update to salmon 0.8.2 because in Bioconda it requires icu 58, while r-base 3.3.1 requires icu 54 --> <requirement type="package" version="0.8.1">salmon</requirement> + <requirement type="package" version="0.43.1">kallisto</requirement> </expand> <command detect_errors="aggressive"><![CDATA[ ln -f -s '$transcripts' input.fa && @@ -125,6 +126,7 @@ <option value="RSEM">RSEM</option> <option value="eXpress">eXpress</option> <option value="salmon">Salmon</option> + <option value="kallisto">Kallisto</option> </param> <when value="RSEM"> <param type="select" name="aln_method" argument="--aln_method" label="Alignment method"> @@ -144,6 +146,8 @@ <option value="fmd">FMD</option> </param> </when> + <when value="kallisto"> + </when> </conditional> <section name="additional_params" title="Additional Options" expanded="False"> @@ -182,6 +186,13 @@ <data format="tabular" name="genes_counts_salmon" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/quant.sf.genes"> <filter>method['est_method'] == "salmon"</filter> </data> + + <data format="tabular" name="isoforms_counts_kallisto" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/abundance.tsv"> + <filter>method['est_method'] == "kallisto"</filter> + </data> + <data format="tabular" name="genes_counts_kallisto" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/abundance.tsv.genes"> + <filter>method['est_method'] == "kallisto"</filter> + </data> </outputs> <tests> <test> @@ -250,8 +261,7 @@ </assert_contents> </output> </test> - <!-- test disabled because broken in travis, probably due to conda/symlink problem--> - <!--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"/> @@ -272,7 +282,28 @@ <has_n_columns n="5" /> </assert_contents> </output> - </test--> + </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="library_type" value="RF"/> + <param name="est_method" value="kallisto"/> + <param name="has_gene_map" value="yes"/> + <output name="isoforms_counts_kallisto"> + <assert_contents> + <has_line_matching expression="TRINITY_DN1_c0_g1_i1	.*" /> + <has_n_columns n="5" /> + </assert_contents> + </output> + <output name="genes_counts_kallisto"> + <assert_contents> + <has_line_matching expression="TRINITY_DN1_c0_g1	.*" /> + <has_n_columns n="5" /> + </assert_contents> + </output> + </test> </tests> <help> <![CDATA[
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/kallisto/abundance.tsv Mon Aug 28 16:54:12 2017 -0400 @@ -0,0 +1,8 @@ +target_id length eff_length est_counts tpm +TRINITY_DN1_c0_g1_i1 380 133.091 13 114025 +TRINITY_DN0_c0_g1_i1 229 31.75 7 257370 +TRINITY_DN2_c0_g1_i1 279 55.7143 1 20952.6 +TRINITY_DN2_c1_g1_i1 541 279.667 15 62611.6 +TRINITY_DN2_c2_g1_i1 240 42.75 4 109227 +TRINITY_DN2_c3_g1_i1 202 19 0 0 +TRINITY_DN3_c0_g1_i1 216 18.75 7 435814
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/kallisto/abundance.tsv.genes Mon Aug 28 16:54:12 2017 -0400 @@ -0,0 +1,8 @@ +target_id length eff_length est_counts tpm +TRINITY_DN3_c0_g1 216.00 18.75 7.00 435814.00 +TRINITY_DN2_c2_g1 240.00 42.75 4.00 109227.00 +TRINITY_DN2_c3_g1 202.00 19.00 0.00 0.00 +TRINITY_DN0_c0_g1 229.00 31.75 7.00 257370.00 +TRINITY_DN2_c0_g1 279.00 55.71 1.00 20952.60 +TRINITY_DN1_c0_g1 380.00 133.09 13.00 114025.00 +TRINITY_DN2_c1_g1 541.00 279.67 15.00 62611.60
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/kallisto/abundance_B.tsv Mon Aug 28 16:54:12 2017 -0400 @@ -0,0 +1,8 @@ +target_id length eff_length est_counts tpm +TRINITY_DN1_c0_g1_i1 229 31.75 7 257370 +TRINITY_DN0_c0_g1_i1 380 133.091 13 114025 +TRINITY_DN2_c0_g1_i1 279 55.7143 1 20952.6 +TRINITY_DN2_c2_g1_i1 541 279.667 15 62611.6 +TRINITY_DN2_c1_g1_i1 240 42.75 4 109227 +TRINITY_DN2_c3_g1_i1 202 19 0 0 +TRINITY_DN3_c0_g1_i1 216 18.75 7 435814
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/kallisto/abundance_B.tsv.genes Mon Aug 28 16:54:12 2017 -0400 @@ -0,0 +1,8 @@ +target_id length eff_length est_counts tpm +TRINITY_DN3_c0_g1 216.00 18.75 7.00 435814.00 +TRINITY_DN2_c1_g1 240.00 42.75 4.00 109227.00 +TRINITY_DN2_c3_g1 202.00 19.00 0.00 0.00 +TRINITY_DN0_c0_g1 380.00 133.09 13.00 114025.00 +TRINITY_DN2_c0_g1 279.00 55.71 1.00 20952.60 +TRINITY_DN1_c0_g1 229.00 31.75 7.00 257370.00 +TRINITY_DN2_c2_g1 541.00 279.67 15.00 62611.60