diff kraken2.xml @ 0:0968856c687c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit 6ad48e582972ec27cdc0d401f877dfe172057231

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/kraken2.xml	Thu Mar 14 05:16:48 2019 -0400
@@ -0,0 +1,147 @@
+<?xml version="1.0"?>
+<tool id="kraken2" name="Kraken2" version="@TOOL_VERSION@+galaxy0">
+    <description>
+        assign taxonomic labels to sequencing reads
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement>
+    </requirements>
+    <version_command>kraken2 --version</version_command>
+    <command detect_errors="exit_code">
+        <![CDATA[
+        kraken2
+            --threads \${GALAXY_SLOTS:-1}
+            --db '${kraken2_database.fields.path}'
+
+            #if $quick:
+                --quick
+            #end if
+
+            #if $single_paired.single_paired_selector == 'yes'
+                --paired
+                '${single_paired.forward_input}' '${single_paired.reverse_input}'
+            #elif $single_paired.single_paired_selector == "collection":
+                '${single_paired.input_pair.forward}' '${single_paired.input_pair.reverse}'
+            #else:
+                '${single_paired.input_sequences}'
+            #end if
+
+            #if $split_reads:
+                --classified-out '${classified_out}' --unclassified-out '${unclassified_out}'
+            #end if
+
+            --confidence '${confidence}'
+	    
+            --minimum-base-quality '${min_base_quality}'
+
+            #if $use_names:
+                --use-names
+            #end if
+
+            #if $report.create_report:
+                --report '${report_output}'
+                #if $report.use_mpa_style:
+                    --use-mpa-style
+                #end if
+                #if $report.report_zero_counts:
+                    --report-zero-counts
+                #end if
+            #end if
+
+            > '${output}'
+    ]]></command>
+    <inputs>
+        <conditional name="single_paired">
+            <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">
+                <option value="collection">Collection</option>
+                <option value="yes">Paired</option>
+                <option selected="True" value="no">Single</option>
+            </param>
+            <when value="collection">
+                <param format="@INTYPES@" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads"/>
+            </when>
+            <when value="yes">
+                <param format="@INTYPES@" name="forward_input" type="data" label="Forward strand"/>
+                <param format="@INTYPES@" name="reverse_input" type="data" label="Reverse strand"/>
+            </when>
+            <when value="no">
+                <param format="@INTYPES@" label="Input sequences" name="input_sequences" type="data"/>
+            </when>
+        </conditional>
+
+    <param name="use_names" type="boolean" label="Print scientific names instead of just taxids"/>
+
+    <param name="confidence"  type="float" label="Confidence" value="0.0" help="Confidence score threshold. Must be in [0, 1]">
+        <validator type="in_range" min="0.0" max="1.0" message="Confidence score threshold should be between 0 and 1" />
+    </param>
+
+    <param name="min_base_quality" type="integer" label="Minimum Base Quality" value="0" help="Minimum base quality used in classification (only effective with FASTQ input)"/>
+	
+    <param name="quick" type="boolean" label="Enable quick operation" help="Quick operation (use first hit)"/>
+
+    <param name="split_reads" type="boolean" label="Split classified and unclassified outputs?" help="Sets --unclassified-out and --classified-out"/>
+
+    <section name="report" title="Create Report" expanded="false">
+        <param name="create_report" type="boolean"  label="Print a report with aggregrate counts/clade to file" help="--report" optional="true"/>
+        <param name="use_mpa_style" type="boolean" label="Format report output like Kraken 1's kraken-mpa-report" help="--use-mpa-style" optional="true"/>
+        <param name="report_zero_counts" type="boolean" label="Report counts for ALL taxa, even if counts are zero" help="--report-zero-counts" optional="true"/>
+    </section>
+
+    <expand macro="input_database"/>
+    
+    </inputs>
+    <outputs>
+        <data name="classified_out" format_source="input_sequences" label="${tool.name} on ${on_string}: Classified reads">
+            <filter>(split_reads)</filter>
+        </data>
+        <data name="unclassified_out" format_source="input_sequences" label="${tool.name} on ${on_string}: Unclassified reads">
+            <filter>(split_reads)</filter>
+        </data>
+    <data name="report_output" format_source="text" label="Report: ${tool.name} on ${on_string}">
+        <filter>(report['create_report'])</filter>
+    </data>
+        <data name="output" format="tabular" label="${tool.name} on ${on_string}: Classification"/>
+        <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />-->
+    </outputs>
+
+    <tests>    
+        <test>
+            <param name="single_paired_selector" value="no"/>
+            <param name="input_sequences" value="kraken_test1.fa" ftype="fasta"/>
+            <param name="split_reads" value="false"/>
+            <param name="quick" value="no"/>
+            <param name="confidence" value=".2"/>
+            <param name="only-classified-output" value="false"/>
+            <param name="kraken2_database" value="test_entry"/>
+            <output name="output" file="kraken_test1_output.tab" ftype="tabular"/>
+        </test>
+    </tests>
+    <help>
+        <![CDATA[
+**What it does**
+
+Kraken2 is a taxonomic sequence classifier that assigns taxonomic labels to short DNA reads. It does this by examining the k-mers within a read and querying a database with those k-mers. This database contains a mapping of every k-mer in Kraken's genomic library to the lowest common ancestor (LCA) in a taxonomic tree of all genomes that contain that k-mer. The set of LCA taxa that correspond to the k-mers in a read are then analyzed to create a single taxonomic label for the read; this label can be any of the nodes in the taxonomic tree. Kraken is designed to be rapid, sensitive, and highly precise.
+
+-----
+
+**Output Format**
+
+Each sequence classified by Kraken results in a single line of output. Output lines contain five tab-delimited fields; from left to right, they are::
+
+    1. "C"/"U": a one letter code indicating that the sequence was either classified or unclassified.
+    2. The sequence ID, obtained from the FASTA/FASTQ header.
+    3. The taxonomy ID Kraken 2 used to label the sequence; this is 0 if the sequence is unclassified.
+    4. The length of the sequence in bp.
+    5. A space-delimited list indicating the LCA mapping of each k-mer in the sequence. For example, "562:13 561:4 A:31 0:1 562:3" would indicate that:
+            a) the first 13 k-mers mapped to taxonomy ID #562
+            b) the next 4 k-mers mapped to taxonomy ID #561
+            c) the next 31 k-mers contained an ambiguous nucleotide
+            d) the next k-mer was not in the database
+            e) the last 3 k-mers mapped to taxonomy ID #562
+        ]]>
+    </help>
+    <expand macro="citations" />
+</tool>