diff obiconvert.xml @ 3:374fd9feb032 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"

--- a/obiconvert.xml	Thu Nov 28 15:51:00 2019 -0500
+++ b/obiconvert.xml	Mon May 10 19:36:34 2021 +0000
@@ -1,113 +1,98 @@
-<tool id="obi_convert" name="obiconvert" version="@TOOL_VERSION@">
-    <description>converts sequence files to different output formats</description>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
-    <expand macro="requirements"/>
-    <expand macro="stdio"/>
-
-    <command>
-        <![CDATA[
-        obiconvert
-        #if $db
-            -d '$db'
-        #end if
-        #if $tax
-            -t '$tax'
-        #end if
-        ${options_inputtype}
-        ${options_seqtype}
-        --${out_format}-output
-        ${uppercase}
-        ${ecopcrdb}
-        #if str( $ecopcrdb) == "--ecopcrdb"
-            --ecopcrdb-output=${ecopcrdb_output}
-        #end if
-        '${input}' > '${output}'
-        ]]>
-
-    </command>
-
-    <inputs>
-        <param name="input" type="data" format="fastq,fasta,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"/>
-        <param name="options_inputtype" type="select" label="Specify the input datatype">
-            <expand macro="inputtype"/>
-        </param>
-        <param name="options_seqtype" type="select" label="Specify the sequence datatype" >
-            <option value="--nuc" selected="true">nucleic</option>
-            <option value="--prot">protein</option>
-        </param>
-        <param name="out_format" type="select" label="Output data type">
-            <option value="fasta" selected="true">fasta</option>
-            <option value="fastq">fastq</option>
-        </param>
-        <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="result.ecopcrdb with ${tool.name} on ${on_string}">
-            <filter>ecopcrdb == True</filter>
-        </data>
-        <data format="fasta" name="output" label="output with ${tool.name} on ${on_string}" >
-            <change_format>
-                <when input="out_format" value="fastq" format="fastq" />
-            </change_format>
-        </data>
-    </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="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>