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Remove deprecated `interpreter attribute from tools <command>`

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This commit is contained in:
Nicola Soranzo
2020-03-05 12:53:09 +01:00
parent 476b194819
commit ef4f5ccda4
29 changed files with 277 additions and 225 deletions
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tools/visualization/LAJ.xml
+30 -27
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@@ -1,20 +1,25 @@
<tool id="laj_1" name="LAJ" version="1.0.0">
<description>Pairwise Alignment Viewer</description>
<command interpreter="python">LAJ.py $maf_input $out_file1</command>
<inputs>
<param name="maf_input" type="data" format="lav" label="Alignment File" optional="False"/>
<param name="seq_file1" type="data" format="fasta" label="First Sequence File" optional="True"/>
<param name="seq_file2" type="data" format="fasta" label="Second Sequence File" optional="True"/>
<param name="exonfile" type="data" format="txt" label="Exon File" optional="True"/>
<param name="repeatfile" type="data" format="txt" label="Repeat File" optional="True"/>
<param name="annotationfile" type="data" format="txt" label="Annotation File" optional="True"/>
<param name="underlayfile" type="data" format="txt" label="Underlay File" optional="True"/>
<param name="highlightfile" type="data" format="txt" label="Highlight File" optional="True"/>
</inputs>
<outputs>
<data name="out_file1" format="laj"/>
</outputs>
<help>
<code file="LAJ_code.py"/>
<command><![CDATA[
python '$__tool_directory__/LAJ.py' '$maf_input' '$out_file1'
]]></command>
<inputs>
<param name="maf_input" type="data" format="lav" label="Alignment File"/>
<param name="seq_file1" type="data" format="fasta" optional="true" label="First Sequence File"/>
<param name="seq_file2" type="data" format="fasta" optional="true" label="Second Sequence File"/>
<param name="exonfile" type="data" format="txt" optional="true" label="Exon File"/>
<param name="repeatfile" type="data" format="txt" optional="true" label="Repeat File"/>
<param name="annotationfile" type="data" format="txt" optional="true" label="Annotation File"/>
<param name="underlayfile" type="data" format="txt" optional="true" label="Underlay File"/>
<param name="highlightfile" type="data" format="txt" optional="true" label="Highlight File"/>
</inputs>
<outputs>
<data name="out_file1" format="laj"/>
</outputs>
<tests>
</tests>
<help><![CDATA[
You can use this tool to view a set of LAV alignments. You may include FASTA formatted sequences for both species.
For detailed information on LAJ, click here_.
@@ -26,17 +31,15 @@ Laj is a tool for viewing and manipulating the output from pairwise alignment pr
.. class:: infomark
**Note:** If you save output from the applet, you will need to manually refresh your history.
</help>
<code file="LAJ_code.py"/>
<citations>
<citation type="bibtex">
@misc{Miller2005,
author = {Miller Lab},
year = {2005},
title = {Laj},
url = {http://globin.bx.psu.edu/dist/laj/},
]]></help>
<citations>
<citation type="bibtex">
@misc{Miller2005,
author = {Miller Lab},
year = {2005},
title = {Laj},
url = {http://globin.bx.psu.edu/dist/laj/},
}
</citation>
</citations>
</citation>
</citations>
</tool>