Mercurial > repos > dfornika > cgview_xml_builder

changeset 0:a3b4d4c9bd51 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
author dfornika
date Thu, 12 Dec 2019 19:32:56 +0000
parents
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files cgview_xml_builder.xml test-data/blastn_output.save.tsv test-data/blastn_output.tsv test-data/blastn_output_reformatted.tsv
diffstat 4 files changed, 81 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cgview_xml_builder.xml	Thu Dec 12 19:32:56 2019 +0000
@@ -0,0 +1,56 @@
+<tool id="cgview_xml_builder" name="cgview XML builder" version="1.0+galaxy0">
+    <description>Circular Genome Viewer</description>
+    <requirements>
+        <requirement type="package" version="1.0">cgview</requirement>
+    </requirements>   
+    <command detect_errors="exit_code">
+        <![CDATA[
+          cgview_xml_builder.pl
+           -gc_content $gc_content
+           -gc_skew $gc_skew
+           -at_content $at_content
+           -at_skew $at_skew
+           -average $average
+           -feature_labels $feature_labels
+           -use_opacity $use_opacity
+           -show_sequence_features $show_sequence_features
+           -sequence '${reference}'
+           -blast '${blast_output}'
+           -output '${output}'
+        ]]>  
+    </command>
+    <inputs>
+        <param name="reference" type="data" format="genbank,fasta" label="Reference" help=""/>
+        <param name="gc_content" type="boolean" truevalue="T" falsevalue="F" label="Display GC Content" checked="true" help=""/>
+	<param name="gc_skew" type="boolean" truevalue="T" falsevalue="F" label="Display GC Skew" checked="false" help=""/>
+	<param name="at_content" type="boolean" truevalue="T" falsevalue="F" label="Display AT Content" checked="false" help=""/>
+	<param name="at_skew" type="boolean" truevalue="T" falsevalue="F" label="Display AT Skew" checked="false" help=""/>
+	<param name="average" type="boolean" truevalue="T" falsevalue="F" label="Display deviation of GC and AT values from the average for the entire genome." checked="true" help=""/>
+	<param name="feature_labels" type="boolean" truevalue="T" falsevalue="F" label="Display feature labels from GenBank file" checked="false" help=""/>
+	<param name="use_opacity" type="boolean" truevalue="T" falsevalue="F" label="Draw BLAST hits with partial opacity" checked="false" help=""/>
+        <param name="show_sequence_features" type="boolean" truevalue="T" falsevalue="F" label="Draw features in the reference (GenBank) file" checked="false" help=""/>
+        <param name="blast_output" type="data" format="tabular" />
+    </inputs>
+    <outputs>
+        <data name="output" format="xml"/> 
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+    </help>
+    <citations>
+        <citation type="bibtex">
+            @article{
+              stothard2004circular,
+              title={Circular genome visualization and exploration using CGView},
+              author={Stothard, Paul and Wishart, David S},
+              journal={Bioinformatics},
+              volume={21},
+              number={4},
+              pages={537--539},
+              year={2004},
+              publisher={Oxford University Press}
+            }
+    </citation>
+  </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/blastn_output.save.tsv	Thu Dec 12 19:32:56 2019 +0000
@@ -0,0 +1,8 @@
+LR595890.1_segment	LR595890.1	100.00	9180	0	0	1	9180	23821	33000	0.0	16556
+LR595890.1_segment	LR595890.1	75.25	198	49	0	7921	8118	31621	31818	8e-33	136
+LR595890.1_segment	LR595890.1	75.25	198	49	0	7801	7998	31741	31938	8e-33	136
+LR595890.1_segment	LR595890.1	89.61	77	6	1	1312	1388	56503	56577	6e-22	100
+LR595890.1_segment	LR595890.1	74.17	120	31	0	7915	8034	30388	30507	7e-15	77.0
+LR595890.1_segment	LR595890.1	74.17	120	31	0	6568	6687	31735	31854	7e-15	77.0
+LR595890.1_segment	LR595890.1	84.29	70	7	2	1326	1393	56585	56518	3e-13	71.6
+LR595890.1_segment	LR595890.1	79.76	84	8	5	1312	1389	89049	89129	5e-10	60.8
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/blastn_output.tsv	Thu Dec 12 19:32:56 2019 +0000
@@ -0,0 +1,8 @@
+LR595890.1_segment	LR595890.1	100.00	9180	0	0	1	9180	23821	33000	0.0	16556
+LR595890.1_segment	LR595890.1	75.25	198	49	0	7921	8118	31621	31818	8e-33	136
+LR595890.1_segment	LR595890.1	75.25	198	49	0	7801	7998	31741	31938	8e-33	136
+LR595890.1_segment	LR595890.1	89.61	77	6	1	1312	1388	56503	56577	6e-22	100
+LR595890.1_segment	LR595890.1	74.17	120	31	0	7915	8034	30388	30507	7e-15	77.0
+LR595890.1_segment	LR595890.1	74.17	120	31	0	6568	6687	31735	31854	7e-15	77.0
+LR595890.1_segment	LR595890.1	84.29	70	7	2	1326	1393	56585	56518	3e-13	71.6
+LR595890.1_segment	LR595890.1	79.76	84	8	5	1312	1389	89049	89129	5e-10	60.8
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/blastn_output_reformatted.tsv	Thu Dec 12 19:32:56 2019 +0000
@@ -0,0 +1,9 @@
+query_id	match_id	match_description	%_identity	alignment_length	mismatches	gap_openings	q_start	q_end	s_start	s_end	evalue	bit_score
+LR595890.1_segment	LR595890.1	match	100.00	9180	0	0	1	9180	23821	33000	0.0	16556
+LR595890.1_segment	LR595890.1	match	75.25	198	49	0	7921	8118	31621	31818	8e-33	136
+LR595890.1_segment	LR595890.1	match	75.25	198	49	0	7801	7998	31741	31938	8e-33	136
+LR595890.1_segment	LR595890.1	match	89.61	77	6	1	1312	1388	56503	56577	6e-22	100
+LR595890.1_segment	LR595890.1	match	74.17	120	31	0	7915	8034	30388	30507	7e-15	77.0
+LR595890.1_segment	LR595890.1	match	74.17	120	31	0	6568	6687	31735	31854	7e-15	77.0
+LR595890.1_segment	LR595890.1	match	84.29	70	7	2	1326	1393	56585	56518	3e-13	71.6
+LR595890.1_segment	LR595890.1	match	79.76	84	8	5	1312	1389	89049	89129	5e-10	60.8