| Previous changeset 6:53d74155bb52 (2020-07-13) Next changeset 8:04b494623f8e (2020-10-03) |
|
Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6" |
|
modified:
alevin.xml vpolo_convert.py |
|
added:
test-data/alevin_mat.mtx |
|
removed:
test-data/alevin_mat.mtx.gz |
| b |
| diff -r 53d74155bb52 -r ff78e9c7b0d8 alevin.xml --- a/alevin.xml Mon Jul 13 17:14:54 2020 -0400 +++ b/alevin.xml Sat Oct 03 18:21:49 2020 +0000 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="alevin" name="Alevin" version="@VERSION@+galaxy1">\n+<tool id="alevin" name="Alevin" version="@VERSION@+galaxy2">\n <description>Quantification and analysis of 3\xe2\x80\x99 tagged-end single-cell sequencing data</description>\n <macros>\n <import>macros.xml</import>\n@@ -97,11 +97,23 @@\n \n #if $optional.dumpMtx != "--dumpMtx":\n && python \'$__tool_directory__/vpolo_convert.py\' -m\n+ #else:\n+ && gunzip output/alevin/quants_mat.mtx.gz\n #end if\n #if $optional.dumpUmiGraph:\n && python \'$__tool_directory__/vpolo_convert.py\' -u\n && sh \'$__tool_directory__/umiout.sh\'\n #end if\n+\n+ && gunzip output/alevin/quants_tier_mat.gz\n+ #if $optional.numCellBootstraps:\n+ && gunzip output/alevin/quants_mean_mat.gz\n+ && gunzip output/alevin/quants_var_mat.gz\n+ #end if\n+\n+ && gunzip output/aux_info/fld.gz\n+ && gunzip output/aux_info/observed_bias.gz\n+ && gunzip output/aux_info/observed_bias_3p.gz\n ]]>\n </command>\n <inputs>\n@@ -144,7 +156,8 @@\n <param name="forceCells" type="integer" optional="true" help="Explicitly specify the number of cells."/>\n <param name="expectCells" type="integer" optional="true" help="define a close upper bound on expected number of cells."/>\n <param name="numCellBootstraps" type="integer" optional="true" help="Performs certain number of bootstrap and generate the mean and variance of the count matrix"/>\n- <param name="minScoreFraction" type="float" optional="true" help="This value controls the minimum allowed score for a mapping to be considered valid. It matters only when --validateMappings has been passed to Salmon. The maximum possible score for a fragment is ms = read_len * ma (or ms = (left_read_len + right_read_len) * ma for paired-end reads). The argument to --minScoreFraction determines what fraction of the maximum score s a mapping must achieve to be potentially retained. For a minimum score fraction of f, only mappings with a score less than (f * s) will be kept. Mappings with lower scores will be considered as low-quality, and will be discarded."/>\n+ <param name="minScoreFraction" type="float" optional="true" help="This value controls the minimum allowed score for a mapping to be considered valid. It matters only when --validateMappings has been passed to Salmon. The maximum possible score for a fragment is ms = read_len * ma (or ms = (left_read_len + right_read_len) * ma for paired-end reads).\n+ The argument to --minScoreFraction determines what fraction of the maximum score s a mapping must achieve to be potentially retained. For a minimum score fraction of f, only mappings with a score less than (f * s) will be kept. Mappings with lower scores will be considered as low-quality, and will be discarded."/>\n <param name="keepCBFraction" type="float" optional="true" help="Fraction of cellular barcodes to keep (Between 0 and 1)."/>\n <param name="lowRegionMinNumBarcodes" type="integer" optional="true" help="Minimum number of cell barcodes to use fo learning low confidence region (defaults to 200)"/>\n <param name="maxNumBarcodes" type="integer" optional="true" help="Maximum allowable limit to process the cell barcodes. Defaults to 100000"/>\n@@ -155,7 +168,7 @@\n <data name="quants_mat.tsv" label="quants_mat.tsv" format="txt" from_work_dir="quants_mat.tsv">\n <filter>optional["dumpMtx"] is not True</filter>\n </data>\n- <data name="quants_mat.mtx.gz" label="quants_mat.mtx.gz" format="mtx" from_work_dir="output/alevin/quants_mat.mtx.gz">\n+ <data name="quants_mat.mtx" label="quants_mat.mtx" format="mtx" from_work_dir="output/alevin/quants_mat.mtx">\n <filter>optional["dumpMtx"]</filter>\n </data>\n <data name="raw_cb_frequency.txt" label="raw_cb_frequency.txt" '..b'alevin.log" format="txt" from_work_dir="output/alevin/alevin.log">\n <filter>allout</filter>\n </data>\n@@ -172,10 +185,10 @@\n <data name="bfh.txt" label="bfh.txt" format="txt" from_work_dir="output/alevin/bfh.txt">\n <filter>optional["dumpBfh"]</filter>\n </data>\n- <data name="quants_mean_mat.gz" label="quants_mean_mat.gz" format="mtx" from_work_dir="output/alevin/quants_mean_mat.gz">\n+ <data name="quants_mean_mat" label="quants_mean_mat" format="mtx" from_work_dir="output/alevin/quants_mean_mat">\n <filter>optional["numCellBootstraps"]</filter>\n </data>\n- <data name="quants_var_mat.gz" label="quants_var_mat.gz" format="mtx" from_work_dir="output/alevin/quants_var_mat.gz">\n+ <data name="quants_var_mat" label="quants_var_mat" format="mtx" from_work_dir="output/alevin/quants_var_mat">\n <filter>optional["numCellBootstraps"]</filter>\n </data>\n <data name="quants_boot_rows.txt" label="quants_boot_rows.txt" format="txt" from_work_dir="output/alevin/quants_boot_rows.txt">\n@@ -190,9 +203,9 @@\n <data name="meta_info.json" format="json" label="meta_info.json" from_work_dir="output/aux_info/meta_info.json">\n <filter>allout</filter>\n </data>\n- <data name="expected_bias.gz" format="txt" label="expected_bias.gz" from_work_dir="output/aux_info/fld.gz"/>\n- <data name="observed_bias.gz" format="txt" label="observed_bias.gz" from_work_dir="output/aux_info/observed_bias.gz"/>\n- <data name="observed_bias_3p.gz" format="txt" label="observed_bias_3p.gz" from_work_dir="output/aux_info/observed_bias_3p.gz"/>\n+ <data name="expected_bias" format="txt" label="expected_bias" from_work_dir="output/aux_info/fld"/>\n+ <data name="observed_bias" format="txt" label="observed_bias" from_work_dir="output/aux_info/observed_bias"/>\n+ <data name="observed_bias_3p" format="txt" label="observed_bias_3p" from_work_dir="output/aux_info/observed_bias_3p"/>\n <data name="flenDist.txt" format="txt" label="flenDist.txt" from_work_dir="output/libParams/flenDist.txt"/>\n <data name="salmon_quant.log" format="txt" label="salmon_quant.log" from_work_dir="output/logs/salmon_quant.log">\n <filter>allout</filter>\n@@ -223,7 +236,32 @@\n <param name="freqThreshold" value="5"/>\n <param name="dumpFeatures" value="Yes"/>\n <param name="keepCBFraction" value="1"/>\n- <output name="quants_mat.mtx.gz" file="alevin_mat.mtx.gz" ftype="mtx" compare="sim_size"/>\n+ <output name="quants_mat.mtx" file="alevin_mat.mtx" ftype="mtx"/>\n+ </test>\n+ <test expect_num_outputs="14">\n+ <conditional name="refTranscriptSource">\n+ <param name="TranscriptSource" value="history"/>\n+ <section name="s_index">\n+ <param name="fasta" value="minitranscript.fa"/>\n+ </section>\n+ </conditional>\n+ <conditional name="pairstraight">\n+ <param name="readselect" value="paired"/>\n+ <param name="file1" value="fastqs/moreminifastq1.fastq.gz"/>\n+ <param name="file2" value="fastqs/moreminifastq2.fastq.gz"/>\n+ <param name="orientation" value="I"/>\n+ <param name="strandedness" value="SR"/>\n+ </conditional>\n+ <param name="protocol" value="--chromium"/>\n+ <param name="tgmap" value="minitxp.tsv"/>\n+ <param name="dumpMtx" value="Yes"/>\n+ <param name="freqThreshold" value="5"/>\n+ <param name="dumpFeatures" value="Yes"/>\n+ <param name="keepCBFraction" value="1"/>\n+ <section name="optional">\n+ <param name="numCellBootstraps" value="2"/>\n+ </section>\n+ <output name="quants_mat.mtx" file="alevin_mat.mtx" ftype="mtx"/>\n </test>\n </tests>\n <help><![CDATA[\n' |
| b |
| diff -r 53d74155bb52 -r ff78e9c7b0d8 test-data/alevin_mat.mtx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alevin_mat.mtx Sat Oct 03 18:21:49 2020 +0000 |
| b |
| @@ -0,0 +1,101 @@ +%%MatrixMarket matrix coordinate real general +95 61 99 +1 9 1.000000 +2 28 1.000000 +3 38 1.000000 +4 28 1.000000 +5 42 1.000000 +6 9 1.000000 +7 56 1.000000 +8 28 1.000000 +9 28 1.000000 +10 30 1.000000 +11 53 1.000000 +12 4 1.000000 +13 28 1.000000 +14 56 1.000000 +15 9 1.000000 +16 43 0.500000 +16 45 0.500000 +17 42 0.500000 +17 44 0.500000 +18 28 1.000000 +19 46 1.000000 +20 38 1.000000 +21 40 1.000000 +22 19 1.000000 +23 9 1.000000 +24 56 1.000000 +25 8 1.000000 +26 28 1.000000 +27 53 1.000000 +28 56 1.000000 +29 28 1.000000 +30 30 1.000000 +31 38 1.000000 +32 28 1.000000 +33 30 1.000000 +34 34 1.000000 +35 30 1.000000 +36 28 1.000000 +37 34 1.000000 +38 16 1.000000 +39 19 1.000000 +40 47 1.000000 +41 38 1.000000 +42 28 1.000000 +43 56 1.000000 +44 28 1.000000 +45 9 1.000000 +46 19 1.000000 +47 23 1.000000 +48 43 0.500000 +48 45 0.500000 +49 38 1.000000 +50 57 1.000000 +51 40 1.000000 +52 38 1.000000 +53 19 1.000000 +54 16 1.000000 +55 15 1.000000 +56 56 1.000000 +57 53 1.000000 +58 30 1.000000 +59 9 1.000000 +60 34 1.000000 +61 30 1.000000 +62 24 1.000000 +63 30 1.000000 +64 56 1.000000 +65 9 1.000000 +66 23 1.000000 +67 61 1.000000 +68 38 1.000000 +69 21 1.000000 +70 38 1.000000 +71 38 1.000000 +72 16 1.000000 +73 30 1.000000 +74 16 1.000000 +75 30 1.000000 +76 40 1.000000 +77 52 1.000000 +78 53 1.000000 +79 42 0.500000 +79 44 0.500000 +80 34 1.000000 +81 9 1.000000 +82 15 1.000000 +83 45 1.000000 +84 47 1.000000 +85 40 1.000000 +86 56 1.000000 +87 56 1.000000 +88 34 1.000000 +89 56 1.000000 +90 38 1.000000 +91 53 1.000000 +92 56 1.000000 +93 53 1.000000 +94 38 1.000000 +95 53 1.000000 |
| b |
| diff -r 53d74155bb52 -r ff78e9c7b0d8 test-data/alevin_mat.mtx.gz |
| b |
| Binary file test-data/alevin_mat.mtx.gz has changed |
| b |
| diff -r 53d74155bb52 -r ff78e9c7b0d8 vpolo_convert.py --- a/vpolo_convert.py Mon Jul 13 17:14:54 2020 -0400 +++ b/vpolo_convert.py Sat Oct 03 18:21:49 2020 +0000 |
| b |
| @@ -1,8 +1,9 @@ #!/usr/bin/env python +import argparse +import os from vpolo.alevin import parser as par -import argparse -import os + parser = argparse.ArgumentParser() parser.add_argument("--mtx", "-m", action="store_true", help="--dumpMtx flag set") |