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changeset 4:e328ced6cf0a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
author iuc
date Wed, 20 Mar 2024 13:15:46 +0000
parents 374fd9feb032
children
files macros.xml obiconvert.xml test-data/input_ngsfilter_extrafile.txt
diffstat 3 files changed, 108 insertions(+), 103 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Mon May 10 19:36:34 2021 +0000
+++ b/macros.xml	Wed Mar 20 13:15:46 2024 +0000
@@ -5,7 +5,11 @@
             <requirement type="package" version="@TOOL_VERSION@">obitools</requirement>
         </requirements>
     </xml>
-
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">obitools</xref>
+        </xrefs>
+    </xml>
     <token name="@TOOL_VERSION@">1.2.13</token>
     <token name="@PROFILE@">21.01</token>
 
--- a/obiconvert.xml	Mon May 10 19:36:34 2021 +0000
+++ b/obiconvert.xml	Wed Mar 20 13:15:46 2024 +0000
@@ -1,98 +1,99 @@
-<tool id="obi_convert" name="obiconvert" version="@TOOL_VERSION@" profile="@PROFILE@">
-    <description>converts sequence files to different output formats</description>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
-    <expand macro="requirements"/>
-    <expand macro="stdio"/>
-    <command><![CDATA[
-        @GUNZIP_INPUT@
-        
-        obiconvert
-        #if $db
-            -d '$db'
-        #end if
-        #if $tax
-            -t '$tax'
-        #end if
-        @INPUT_FORMAT@
-        @OUT_FORMAT@
-        ${uppercase}
-        ${ecopcrdb}
-        #if str( $ecopcrdb) == "--ecopcrdb"
-            --ecopcrdb-output=${ecopcrdb_output}
-        #end if
-        input 
-        @GZIP_OUTPUT@
-        > '${output}'
-        @GENERATE_GALAXY_JSON@
-    ]]></command>
-    <inputs>
-        <param name="input" type="data" format="@INPUT_FORMATS@,txt,tabular" label="Input sequences file" help="database used for the in silico PCR. The database must be in the ecoPCR format (for example output of obiconvert)" />
-        <param name="db" type="data" optional="true" format="txt,tabular" label="ecoPCR taxonomy database" />
-        <param name="tax" type="data" optional="true" format="txt,tabular" label="NCBI taxonomy dump repository"/>
-        <expand macro="input_format_options_macro"/>
-        <expand macro="out_format_macro"/>
-        <param name="ecopcrdb" type="boolean" truevalue="--ecopcrdb" falsevalue="" label="Do you want to create an ecoPCR database from sequence records results?"  help="Use this option if you want to generate an ecoPCR database output file" />
-        <param name="uppercase" type="boolean" truevalue="--uppercase" falsevalue=""  label="Do you want to print sequences in upper case?" />
-    </inputs>
-    <outputs>
-        <data format="txt" name="ecopcrdb_output" label="${tool.name} on ${on_string}: ecopcrdb">
-            <filter>ecopcrdb == True</filter>
-        </data>
-        <data format="auto" name="output"/>
-    </outputs>
-    <tests>
-        <test>
-            <param name="input" value="output_obisort.fasta" />
-            <param name="options_inputtype" value="--fasta"/>
-            <param name="options_seqtype" value="--nuc"/>
-            <param name="out_format" value="fasta"/>
-            <param name="ecopcrdb" value="false"/>
-            <param name="uppercase" value="true"/>
-            <output name="output" file="output_obiconvert.fasta" ftype="fasta"/>
-        </test>
-    </tests>
-    <help><![CDATA[
-
-.. class:: infomark
-
-**What it does**
-
-obiconvert converts sequence files to different output formats. See the documentation for more details on the different formats.
-
-Input files can be in :
-
-fasta format
-
-extended OBITools fasta format
-
-Sanger fastq format
-
-Solexa fastq format
-
-ecoPCR format
-
-ecoPCR database format
-
-GenBank format
-
-EMBL format
-
-obiconvert converts those files to the :
-
-extended OBITools fasta format
-
-Sanger fastq format
-
-ecoPCR database format
-
-If no file name is specified, data is read from standard input.
-
-@OBITOOLS_LINK@
-
-    ]]>
-
-    </help>
-    <expand macro="citation" />
-</tool>
+<tool id="obi_convert" name="obiconvert" version="@TOOL_VERSION@" profile="@PROFILE@">
+    <description>converts sequence files to different output formats</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="bio_tools"/>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <command><![CDATA[
+        @GUNZIP_INPUT@
+        
+        obiconvert
+        #if $db
+            -d '$db'
+        #end if
+        #if $tax
+            -t '$tax'
+        #end if
+        @INPUT_FORMAT@
+        @OUT_FORMAT@
+        ${uppercase}
+        ${ecopcrdb}
+        #if str( $ecopcrdb) == "--ecopcrdb"
+            --ecopcrdb-output=${ecopcrdb_output}
+        #end if
+        input 
+        @GZIP_OUTPUT@
+        > '${output}'
+        @GENERATE_GALAXY_JSON@
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="@INPUT_FORMATS@,txt,tabular" label="Input sequences file" help="database used for the in silico PCR. The database must be in the ecoPCR format (for example output of obiconvert)"/>
+        <param name="db" type="data" optional="true" format="txt,tabular" label="ecoPCR taxonomy database"/>
+        <param name="tax" type="data" optional="true" format="txt,tabular" label="NCBI taxonomy dump repository"/>
+        <expand macro="input_format_options_macro"/>
+        <expand macro="out_format_macro"/>
+        <param name="ecopcrdb" type="boolean" truevalue="--ecopcrdb" falsevalue="" label="Do you want to create an ecoPCR database from sequence records results?"  help="Use this option if you want to generate an ecoPCR database output file"/>
+        <param name="uppercase" type="boolean" truevalue="--uppercase" falsevalue=""  label="Do you want to print sequences in upper case?"/>
+    </inputs>
+    <outputs>
+        <data format="txt" name="ecopcrdb_output" label="${tool.name} on ${on_string}: ecopcrdb">
+            <filter>ecopcrdb == True</filter>
+        </data>
+        <data format="auto" name="output"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input" value="output_obisort.fasta" />
+            <param name="options_inputtype" value="--fasta"/>
+            <param name="options_seqtype" value="--nuc"/>
+            <param name="out_format" value="fasta"/>
+            <param name="ecopcrdb" value="false"/>
+            <param name="uppercase" value="true"/>
+            <output name="output" file="output_obiconvert.fasta" ftype="fasta"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What it does**
+
+obiconvert converts sequence files to different output formats. See the documentation for more details on the different formats.
+
+Input files can be in :
+
+fasta format
+
+extended OBITools fasta format
+
+Sanger fastq format
+
+Solexa fastq format
+
+ecoPCR format
+
+ecoPCR database format
+
+GenBank format
+
+EMBL format
+
+obiconvert converts those files to the :
+
+extended OBITools fasta format
+
+Sanger fastq format
+
+ecoPCR database format
+
+If no file name is specified, data is read from standard input.
+
+@OBITOOLS_LINK@
+
+    ]]>
+
+    </help>
+    <expand macro="citation" />
+</tool>
--- a/test-data/input_ngsfilter_extrafile.txt	Mon May 10 19:36:34 2021 +0000
+++ b/test-data/input_ngsfilter_extrafile.txt	Wed Mar 20 13:15:46 2024 +0000
@@ -1,4 +1,4 @@
-wolf_diet    13a_F730603      aattaac  TTAGATACCCCACTATGC    TAGAACAGGCTCCTCTAG     F       @
-wolf_diet    15a_F730814      gaagtag  TTAGATACCCCACTATGC    TAGAACAGGCTCCTCTAG     F       @
-wolf_diet    26a_F040644      gaatatc  TTAGATACCCCACTATGC    TAGAACAGGCTCCTCTAG     F       @
-wolf_diet    29a_F260619      gcctcct  TTAGATACCCCACTATGC    TAGAACAGGCTCCTCTAG     F       @
+wolf_diet	13a_F730603	aattaac	TTAGATACCCCACTATGC	TAGAACAGGCTCCTCTAG	F	@
+wolf_diet	15a_F730814	gaagtag	TTAGATACCCCACTATGC	TAGAACAGGCTCCTCTAG	F	@
+wolf_diet	26a_F040644	gaatatc	TTAGATACCCCACTATGC	TAGAACAGGCTCCTCTAG	F	@
+wolf_diet	29a_F260619	gcctcct	TTAGATACCCCACTATGC	TAGAACAGGCTCCTCTAG	F	@