Mercurial > repos > iuc > parse_mito_blast

changeset 0:f172b1f77d6c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast commit 26909099e5c61564bd72f67974e30e75f3fad22c
author iuc
date Thu, 12 May 2022 10:45:45 +0000
parents
children 3c9ad4adf8d2
files parse_mito_blast.xml test-data/test_cov_report.tsv test-data/test_input.tsv test-data/test_mito_scaff_names.txt
diffstat 4 files changed, 315 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /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>
--- /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
@@ -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
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+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
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+59	SCAFFOLD_266	NC_015195.1	33195	32637	98.31902394938997
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+50	SCAFFOLD_266	NC_053917.1	33195	32580	98.14731134206959
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+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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_input.tsv	Thu May 12 10:45:45 2022 +0000
@@ -0,0 +1,200 @@
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+SCAFFOLD_266	NC_053066.1	3457	1	3435	0.0	33195	99	10
+SCAFFOLD_266	NC_015898.1	16653	3729	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_015898.1	12683	20584	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_015898.1	3452	1	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_057294.1	16729	3668	20290	0.0	33195	99	50
+SCAFFOLD_266	NC_057294.1	12746	20523	33195	0.0	33195	99	38
+SCAFFOLD_266	NC_057294.1	3458	2	3435	0.0	33195	99	10
+SCAFFOLD_266	NC_014455.1	16662	3713	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_014455.1	12688	20568	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_014455.1	3450	1	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_053053.1	16620	3767	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_053053.1	12648	20622	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_053053.1	3455	1	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_020423.1	16627	3771	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_020423.1	12654	20626	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_020423.1	3451	2	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_015237.1	16650	3729	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_015237.1	12676	20584	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_015237.1	3452	1	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_015613.1	16660	3713	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_015613.1	12688	20568	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_015613.1	3451	1	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_053059.1	16632	3771	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_053059.1	12659	20626	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_053059.1	3451	1	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_015074.1	16657	3747	20285	0.0	33195	98	50
+SCAFFOLD_266	NC_015074.1	12668	20602	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_015074.1	3457	1	3430	0.0	33195	98	10
+SCAFFOLD_266	NC_053917.1	16650	3742	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_053917.1	12667	20597	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_053917.1	3464	1	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_015232.1	16628	3743	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_015232.1	12653	20598	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_015232.1	3458	1	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_054298.1	16640	3753	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_054298.1	12666	20608	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_054298.1	3460	1	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_014341.1	16628	3766	20285	0.0	33195	98	50
+SCAFFOLD_266	NC_014341.1	12646	20621	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_014341.1	3457	1	3430	0.0	33195	98	10
+SCAFFOLD_266	NC_015802.1	16648	3747	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_015802.1	12671	20602	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_015802.1	3461	1	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_057295.1	16684	3715	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_057295.1	12704	20570	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_057295.1	3453	5	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_053061.1	16597	3794	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_053061.1	12616	20649	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_053061.1	3460	1	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_052841.1	15643	4711	20290	0.0	33195	96	47
+SCAFFOLD_266	NC_052841.1	11665	21566	33195	0.0	33195	96	35
+SCAFFOLD_266	NC_052841.1	3452	8	3435	0.0	33195	96	10
+SCAFFOLD_266	NC_052841.1	624	20626	21231	4.08e-94	33195	96	2
+SCAFFOLD_266	NC_052841.1	624	3771	4376	4.08e-94	33195	96	2
+SCAFFOLD_266	NC_052843.1	16624	3766	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_052843.1	12653	20621	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_052843.1	3449	5	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_015195.1	16656	3713	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_015195.1	12686	20568	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_015195.1	3448	2	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_053050.1	16671	3729	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_053050.1	12699	20584	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_053050.1	3452	1	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_057250.1	16607	3771	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_057250.1	12640	20626	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_057250.1	3448	1	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_053077.1	16654	3729	20290	0.0	33195	98	50
+SCAFFOLD_266	NC_053077.1	12680	20584	33195	0.0	33195	98	38
+SCAFFOLD_266	NC_053077.1	3456	2	3435	0.0	33195	98	10
+SCAFFOLD_266	NC_058320.1	15651	4711	20291	0.0	33195	96	47
+SCAFFOLD_266	NC_058320.1	11675	21566	33195	0.0	33195	96	35
+SCAFFOLD_266	NC_058320.1	3459	1	3436	0.0	33195	96	10
--- /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
@@ -0,0 +1,1 @@
+SCAFFOLD_266
\ No newline at end of file