Mercurial > repos > bgruening > alevin
changeset 4:917f8e439160 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 5dfee8ad03865f59c3e1ac9dd5865fd40e4616ef"
author | bgruening |
---|---|
date | Wed, 06 Nov 2019 13:54:21 -0500 |
parents | 0a5258e41227 |
children | e572598580c2 |
files | alevin.xml |
diffstat | 1 files changed, 12 insertions(+), 2 deletions(-) [+] |
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line diff
--- a/alevin.xml Thu Oct 17 17:05:18 2019 -0400 +++ b/alevin.xml Wed Nov 06 13:54:21 2019 -0500 @@ -1,4 +1,4 @@ -<tool id="alevin" name="Alevin" version="@VERSION@"> +<tool id="alevin" name="Alevin" version="@VERSION@+galaxy1"> <description>Quantification and analysis of 3’ tagged-end single-cell sequencing data</description> <macros> <import>macros.xml</import> @@ -91,6 +91,9 @@ #if $optional.maxNumBarcodes: --maxNumBarcodes '${optional.maxNumBarcodes}' #end if + #if $optional.freqThreshold: + --freqThreshold '${optional.freqThreshold}' + #end if #if $optional.dumpMtx != "--dumpMtx": && python '$__tool_directory__/vpolo_convert.py' -m @@ -145,6 +148,7 @@ <param name="keepCBFraction" type="float" optional="true" help="Fraction of cellular barcodes to keep (Between 0 and 1)."/> <param name="lowRegionMinNumBarcodes" type="integer" optional="true" help="Minimum number of cell barcodes to use fo learning low confidence region (defaults to 200)"/> <param name="maxNumBarcodes" type="integer" optional="true" help="Maximum allowable limit to process the cell barcodes. Defaults to 100000"/> + <param name="freqThreshold" type="integer" optional="true" help="Minimum frequency for a barcode to be considered. Defaults to 10"/> </section> </inputs> <outputs> @@ -154,6 +158,9 @@ <data name="quants_mat.mtx.gz" label="quants_mat.mtx.gz" format="mtx" from_work_dir="output/alevin/quants_mat.mtx.gz"> <filter>optional["dumpMtx"]</filter> </data> + <data name="raw_cb_frequency.txt" label="raw_cb_frequency.txt" format="txt" from_work_dir="output/alevin/raw_cb_frequency.txt"> + <filter>optional["dumpFeatures"]</filter> + </data> <data name="quants_mat_cols.txt" label="quants_mat_cols.txt" format="txt" from_work_dir="output/alevin/quants_mat_cols.txt"/> <data name="quants_mat_rows.txt" label="quants_mat_rows.txt" format="txt" from_work_dir="output/alevin/quants_mat_rows.txt"/> <data name="quants_tier_mat.gz" label="quants_tier_mat.gz" format="mtx" from_work_dir="output/alevin/quants_tier_mat.gz"/> @@ -196,7 +203,7 @@ </collection> </outputs> <tests> - <test expect_num_outputs="10"> + <test expect_num_outputs="11"> <conditional name="refTranscriptSource"> <param name="TranscriptSource" value="history"/> <section name="s_index"> @@ -213,6 +220,9 @@ <param name="protocol" value="--chromium"/> <param name="tgmap" value="minitxp.tsv"/> <param name="dumpMtx" value="Yes"/> + <param name="freqThreshold" value="5"/> + <param name="dumpFeatures" value="Yes"/> + <param name="keepCBFraction" value="1"/> <output name="quants_mat.mtx.gz" file="alevin_mat.mtx.gz" ftype="mtx" compare="sim_size"/> </test> </tests>