Repository 'parse_mito_blast'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/parse_mito_blast

Changeset 0:f172b1f77d6c (2022-05-12)
Next changeset 1:3c9ad4adf8d2 (2022-06-09)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
added:
parse_mito_blast.xml
test-data/test_cov_report.tsv
test-data/test_input.tsv
test-data/test_mito_scaff_names.txt
b
diff -r 000000000000 -r f172b1f77d6c parse_mito_blast.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/parse_mito_blast.xml Thu May 12 10:45:45 2022 +0000
[
@@ -0,0 +1,50 @@
+ <tool id="parse_mito_blast" name="Parse mitochondrial blast" version="@TOOL_VERSION@" profile="21.05">
+    <description>overlap-conscious coverage calculation between scaffold-accession number pairs from blast output</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.0.1</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">parse_mito_blast</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+parse_mito_blast.py
+    --blastout '$blastout' 
+]]>
+    </command>
+    <inputs>
+        <param argument="blastout" type="data" format="tabular" label="Tabular file generated by mito-blast"/>
+    </inputs>
+    <outputs>
+        <data name="cov_report" format="tabular" from_work_dir="cov_report.tsv" label="${tool.name} on ${on_string}" />
+        <data name="mito_scaff_names" format="txt" from_work_dir="mito_scaff_names.txt" label="contaminant scaffolds on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="blastout" value="test_input.tsv" />
+            <output name="cov_report" file="test_cov_report.tsv" ftype="tabular" /> 
+            <output name="mito_scaff_names" file="test_mito_scaff_names.txt" ftype="txt" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+ This tool is intended for use on the tabular (format 6) output generated by blastn. Depending on filtering choices, blast will output \
+ all the alignments it generates. Often there are multiple overlapping alignments for a unique query sequence-accession number pair. This tool \
+ collects all alignments between a given pair and calculates the total coverage between the query and accession number, taking into /
+ account overlapping alignments. Therefore a user can figure out how much of their query sequence actually identifies with a subject /
+ sequence (acc #). This tool was designed for use in the VGP decontamination pipeline - in particular for deciding whether a scaffold /
+ (sequence) is of mitochondrial origin. Parse_mito_blast generates a synthesized, tabular report of coverage for scaffolds with >95% /
+ identity to a mitochondrial subject sequence. To use, pass a format 6 blast output (--blastout) and the desired name of the report. 
+
+ NOTE: This tool is currently designed for use with the blast headers 'qseqid','sseqid','qlen','length','qcovhsp','eval','qstart','qend','qcovs' /
+ and will be sensitive to this order. 
+    ]]>
+    </help>
+    <citations>
+     <citation type="bibtex">
+           @misc{Danecek_et_al,
+           Author={Danecek, P., Schiffels, S., Durbin, R.},
+           title={Multiallelic calling model in bcftools (-m)},
+           url = {http://samtools.github.io/bcftools/call-m.pdf},}
+        </citation>
+    </citations>
+</tool>
b
diff -r 000000000000 -r f172b1f77d6c test-data/test_cov_report.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_cov_report.tsv Thu May 12 10:45:45 2022 +0000
b
@@ -0,0 +1,64 @@
+ Scaffold Acc_number Scaffold_len Scaffold_align_cov Perc_align_cov
+0 SCAFFOLD_266 NC_007897.1 33195 33191 99.98794999246876
+1 SCAFFOLD_266 NC_053065.1 33195 33004 99.42461214038258
+32 SCAFFOLD_266 NC_053079.1 33195 32973 99.33122458201537
+35 SCAFFOLD_266 NC_053073.1 33195 32968 99.3161620726013
+3 SCAFFOLD_266 NC_018827.1 33195 32890 99.08118692574183
+11 SCAFFOLD_266 NC_018794.1 33195 32890 99.08118692574183
+6 SCAFFOLD_266 NC_018812.1 33195 32889 99.07817442385901
+13 SCAFFOLD_266 NC_018796.1 33195 32889 99.07817442385901
+8 SCAFFOLD_266 NC_018807.1 33195 32887 99.0721494200934
+27 SCAFFOLD_266 NC_018810.1 33195 32886 99.06913691821057
+4 SCAFFOLD_266 NC_018806.1 33195 32884 99.06311191444495
+22 SCAFFOLD_266 NC_015198.1 33195 32884 99.06311191444495
+20 SCAFFOLD_266 NC_018798.1 33195 32881 99.05407440879651
+2 SCAFFOLD_266 NC_053082.1 33195 32880 99.0510619069137
+25 SCAFFOLD_266 NC_018802.1 33195 32880 99.0510619069137
+24 SCAFFOLD_266 NC_018808.1 33195 32878 99.04503690314806
+17 SCAFFOLD_266 NC_018801.1 33195 32878 99.04503690314806
+12 SCAFFOLD_266 NC_018803.1 33195 32874 99.03298689561682
+31 SCAFFOLD_266 NC_000880.1 33195 32870 99.02093688808556
+40 SCAFFOLD_266 NC_053066.1 33195 32860 98.99081186925743
+5 SCAFFOLD_266 NC_053083.1 33195 32855 98.97574935984335
+10 SCAFFOLD_266 NC_053084.1 33195 32820 98.87031179394488
+23 SCAFFOLD_266 NC_018797.1 33195 32818 98.86428679017925
+19 SCAFFOLD_266 NC_018813.1 33195 32817 98.86127428829643
+26 SCAFFOLD_266 NC_018795.1 33195 32817 98.86127428829643
+18 SCAFFOLD_266 NC_018809.1 33195 32817 98.86127428829643
+9 SCAFFOLD_266 NC_018799.1 33195 32817 98.86127428829643
+14 SCAFFOLD_266 NC_018811.1 33195 32817 98.86127428829643
+21 SCAFFOLD_266 NC_018805.1 33195 32817 98.86127428829643
+15 SCAFFOLD_266 NC_018804.1 33195 32817 98.86127428829643
+29 SCAFFOLD_266 NC_015234.1 33195 32814 98.85223678264798
+7 SCAFFOLD_266 NC_053110.1 33195 32800 98.8100617562886
+39 SCAFFOLD_266 NC_053645.1 33195 32743 98.63834914896822
+42 SCAFFOLD_266 NC_057294.1 33195 32727 98.5901491188432
+37 SCAFFOLD_266 NC_057247.1 33195 32688 98.47266154541346
+28 SCAFFOLD_266 NC_052840.1 33195 32668 98.41241150775718
+34 SCAFFOLD_266 NC_053068.1 33195 32654 98.3702364813978
+47 SCAFFOLD_266 NC_015613.1 33195 32638 98.3220364512728
+43 SCAFFOLD_266 NC_014455.1 33195 32638 98.3220364512728
+59 SCAFFOLD_266 NC_015195.1 33195 32637 98.31902394938997
+55 SCAFFOLD_266 NC_057295.1 33195 32630 98.29793643621028
+38 SCAFFOLD_266 NC_053109.1 33195 32626 98.28588642867902
+46 SCAFFOLD_266 NC_015237.1 33195 32606 98.22563639102275
+60 SCAFFOLD_266 NC_053050.1 33195 32606 98.22563639102275
+41 SCAFFOLD_266 NC_015898.1 33195 32606 98.22563639102275
+16 SCAFFOLD_266 NC_018800.1 33195 32606 98.22563639102275
+62 SCAFFOLD_266 NC_053077.1 33195 32605 98.22262388913992
+50 SCAFFOLD_266 NC_053917.1 33195 32580 98.14731134206959
+51 SCAFFOLD_266 NC_015232.1 33195 32578 98.14128633830396
+54 SCAFFOLD_266 NC_015802.1 33195 32570 98.11718632324146
+30 SCAFFOLD_266 NC_021408.1 33195 32568 98.11116131947583
+49 SCAFFOLD_266 NC_015074.1 33195 32560 98.08706130441331
+52 SCAFFOLD_266 NC_054298.1 33195 32558 98.08103630064768
+44 SCAFFOLD_266 NC_053053.1 33195 32530 97.9966862479289
+58 SCAFFOLD_266 NC_052843.1 33195 32528 97.99066124416328
+48 SCAFFOLD_266 NC_053059.1 33195 32522 97.9725862328664
+53 SCAFFOLD_266 NC_014341.1 33195 32522 97.9725862328664
+61 SCAFFOLD_266 NC_057250.1 33195 32522 97.9725862328664
+45 SCAFFOLD_266 NC_020423.1 33195 32521 97.96957373098358
+33 SCAFFOLD_266 NC_015233.1 33195 32486 97.8641361650851
+56 SCAFFOLD_266 NC_053061.1 33195 32476 97.83401114625697
+57 SCAFFOLD_266 NC_052841.1 33195 31845 95.93312245820154
+36 SCAFFOLD_266 NC_054361.1 33195 31741 95.61982226238891
b
diff -r 000000000000 -r f172b1f77d6c test-data/test_input.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_input.tsv Thu May 12 10:45:45 2022 +0000
b
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b
diff -r 000000000000 -r f172b1f77d6c test-data/test_mito_scaff_names.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_mito_scaff_names.txt Thu May 12 10:45:45 2022 +0000
b
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