Mercurial > repos > iuc > ucsc_axttomaf
diff axttomaf.xml @ 2:021202bf325f draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf commit 27e5f0847b96c0fef7548d3606dd3958ebda7d1f
| author | iuc |
|---|---|
| date | Thu, 26 Sep 2024 16:52:23 +0000 |
| parents | a030255ee7eb |
| children |
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--- a/axttomaf.xml Sun Sep 22 07:25:16 2024 +0000 +++ b/axttomaf.xml Thu Sep 26 16:52:23 2024 +0000 @@ -1,9 +1,21 @@ -<tool id="ucsc_axtomaf" name="axtToMaf" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT"> +<tool id="ucsc_axtomaf" name="axtToMaf" version="@TOOL_VERSION@+galaxy1" profile="21.05" license="MIT"> <description> Convert dataset from axt to MAF format </description> <macros> <token name="@TOOL_VERSION@">469</token> + <xml name="sanitize_query"> + <sanitizer> + <valid initial="string.printable"> + <remove value=" "/> + <remove value="'" /> + </valid> + <mapping initial="none"> + <add source=" " target=""/> + <add source="'" target="'"'"'"/> + </mapping> + </sanitizer> + </xml> </macros> <xrefs> <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref> @@ -25,6 +37,14 @@ #else: '$query_reference_index_source.que_ref_index_file.fields.path' #end if + #if str($t_prefix) + -tPrefix='$t_prefix' + #end if + #if str($q_prefix) + -qPrefix='$q_prefix' + #end if + $score + $scoreZero '$out' ]]></command> <inputs> @@ -60,6 +80,14 @@ </when> </conditional> + <param name="t_prefix" type="text" optional="true" label="add this to start of TARGET sequence name in maf" help="Typically organism name and a dot (hg38.) is used"> + <expand macro="sanitize_query"/> + </param> + <param name="q_prefix" type="text" optional="true" label="add this to start of QUERY sequence name in maf" help="Typically organism name and a dot (mm10.) is used"> + <expand macro="sanitize_query"/> + </param> + <param argument="-score" type="boolean" truevalue="-score" falsevalue="" label="Recalculate score" /> + <param argument="-scoreZero" type="boolean" truevalue="-scoreZero" falsevalue="" label="Recalculate score if zero" /> </inputs> <outputs> <data name="out" format="maf" /> @@ -78,6 +106,20 @@ <output name="out" file="1.maf"/> </test> <test> + <param name="in_axt" value="2.axt"/> + <conditional name="target_reference_index_source"> + <param name="target_reference_index_source_selector" value="history" /> + <param name="in_tar_ref_index" value="hg38.noprefix.fasta.fai"/> + </conditional> + <conditional name="query_reference_index_source"> + <param name="query_reference_index_source_selector" value="history" /> + <param name="in_que_ref_index" value="mm39.noprefix.fasta.fai"/> + </conditional> + <param name="t_prefix" value="hg38." /> + <param name="q_prefix" value="mm39." /> + <output name="out" file="1.maf"/> + </test> + <test> <param name="in_axt" value="1.axt"/> <conditional name="target_reference_index_source"> <param name="target_reference_index_source_selector" value="cached" />