| Previous changeset 5:8b5039bdf1f6 (2017-03-31) Next changeset 7:34cefa17a764 (2017-12-14) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686 |
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modified:
abundance_estimates_to_matrix.xml |
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added:
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 |
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| diff -r 8b5039bdf1f6 -r 74217fbfba4d abundance_estimates_to_matrix.xml --- a/abundance_estimates_to_matrix.xml Fri Mar 31 11:37:24 2017 -0400 +++ b/abundance_estimates_to_matrix.xml Mon Aug 28 16:55:13 2017 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@WRAPPER_VERSION@.0"> +<tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@WRAPPER_VERSION@.1"> <description>for a de novo assembly of RNA-Seq data by Trinity</description> <macros> <import>macros.xml</import> @@ -7,6 +7,7 @@ <requirement type="package" version="3.16.5">bioconductor-edger</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[ #import re @@ -30,6 +31,7 @@ <option value="RSEM">RSEM</option> <option value="eXpress">eXpress</option> <option value="salmon">Salmon</option> + <option value="kallisto">Kallisto</option> </param> <section name="additional_params" title="Additional Options" expanded="False"> @@ -176,6 +178,29 @@ </assert_contents> </output> </test> + <test> + <param name="samples" ftype="tabular" value="count/kallisto/abundance.tsv.genes,count/kallisto/abundance_B.tsv.genes"/> + <param name="est_method" value="kallisto"/> + <param name="cross_sample_norm" value="TMM"/> + <output name="trans_counts"> + <assert_contents> + <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> + <has_n_columns n="3" /> + </assert_contents> + </output> + <output name="TPM_no_norm"> + <assert_contents> + <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> + <has_n_columns n="3" /> + </assert_contents> + </output> + <output name="norm"> + <assert_contents> + <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> + <has_n_columns n="3" /> + </assert_contents> + </output> + </test> </tests> <help> <![CDATA[ |
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| diff -r 8b5039bdf1f6 -r 74217fbfba4d test-data/count/kallisto/abundance.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/kallisto/abundance.tsv Mon Aug 28 16:55:13 2017 -0400 |
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| @@ -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 |
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| diff -r 8b5039bdf1f6 -r 74217fbfba4d test-data/count/kallisto/abundance.tsv.genes --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/kallisto/abundance.tsv.genes Mon Aug 28 16:55:13 2017 -0400 |
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| @@ -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 |
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| diff -r 8b5039bdf1f6 -r 74217fbfba4d test-data/count/kallisto/abundance_B.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/kallisto/abundance_B.tsv Mon Aug 28 16:55:13 2017 -0400 |
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| @@ -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 |
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| diff -r 8b5039bdf1f6 -r 74217fbfba4d test-data/count/kallisto/abundance_B.tsv.genes --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/kallisto/abundance_B.tsv.genes Mon Aug 28 16:55:13 2017 -0400 |
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| @@ -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 |