changeset 12:4733841a785e draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"

--- a/cgview.xml	Fri Nov 01 21:41:02 2019 -0400
+++ b/cgview.xml	Thu Dec 12 19:31:55 2019 +0000
@@ -8,14 +8,22 @@
           ln -s '${input}' input.xml &&
           cgview
            -i 'input.xml'
-           -o '${output}'
+           -c '${center_zoom_on_base}'
+           -A '${label_font_size}'
+           -z '${zoom_amount}'
+           -s 'outdir'
         ]]>  
     </command>
     <inputs>
         <param name="input" type="data" format="xml" label="Input" help=""/>
+        <param name="center_zoom_on_base" type="integer" min="" value="" max="" label="Base to center zoomed map on" help="" />
+        <param name="label_font_size" type="integer" min="2" value="12" max="96" label="Label font size" help=""/>
+        <param name="zoom_amount" type="integer" min="1" value="1" max="100" label="Zoom amount" help=""/>
     </inputs>
     <outputs>
-        <data name="output" format="png"/> 
+        <data name="output" format="png">
+            <discover_datasets/>
+        </data>
     </outputs>
     <tests>
     </tests>

--- a/cgview_xml_builder.xml	Fri Nov 01 21:41:02 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,56 +0,0 @@
-<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>

--- a/reformat_blastn_output.xml	Fri Nov 01 21:41:02 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-<tool id="reformat_blastn_output" name="reformat blastn output" version="1.0+galaxy0">
-    <description>Reformat blastn output for cgview_xml_builder</description>
-    <requirements>
-    </requirements>   
-    <command detect_errors="exit_code">
-        <![CDATA[
-          awk -F'\t' 'BEGIN {OFS = FS} $2 = $2 FS "match"' '${input}' |
-          sed '1iquery_id\tmatch_id\tmatch_description\t%_identity\talignment_length\tmismatches\tgap_openings\tq_start\tq_end\ts_start\ts_end\tevalue\tbit_score' |
-	  sed '1i#PROGRAM=blastn'
-          > '${output}'
-        ]]>  
-    </command>
-    <inputs>
-        <param name="input" type="data" format="tabular" label="Input" help=""/>
-    </inputs>
-    <outputs>
-        <data name="output" format="tabular"/> 
-    </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>