diff cat_summarise.xml @ 0:0c2e94e8db77 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cat_summarise.xml	Tue Dec 10 21:02:22 2019 +0000
@@ -0,0 +1,87 @@
+<tool id="cat_summarise" name="CAT summarise" version="@VERSION@.0">
+    <description>the number of contigs or bins assigned to each taxonomic name</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <command detect_errors="exit_code"><![CDATA[
+    CAT summarise
+        #if $contigs_fasta
+        -c '$contigs_fasta'
+        #end if
+        -i '$input'
+        -o 'output_names_summary.txt'
+    && @TXT2TSV@ -i 'output_names_summary.txt' -o '$output'
+    ]]></command>
+    <inputs>
+        <param argument="--input" type="data" format="tabular" label="classification.names.txt output from CAT add_names"
+            help="The classication must be made with --only_official names"/>
+        <param argument="--contigs_fasta" type="data" format="fasta" optional="true" label="contigs.fasta used for CAT contigs" 
+            help="Required if summarising a contig2classification.names output derived from CAT contigs"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular" label="#set name = $input.name.replace('.txt','.summary.txt')# ${tool.name} on ${on_string} $name"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" ftype="tabular" value="test_contig.contig2classification.names.txt"/>
+            <param name="contigs_fasta" ftype="fasta" value="contigs.fasta"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="Firmicutes" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+**CAT summarise** 
+
+Summarise taxonomic asignemts from a CAT or BAT classification file that has official taxonomic names added by CAT add_names.
+
+**INPUT**
+
+::
+
+  # bin   classification  reason  lineage lineage scores  superkingdom    phylum  class   order   family  genus   species
+  genome2.fna     classified      based on 6/17 ORFs      1;131567;2;1224;1236;135623;641;662;666 1.00;1.00;1.00;0.89;0.89;0.89;0.89;0.89;0.69    Bacteria: 1.00  Proteobacteria: 0.89    Gammaproteobacteria: 0.89       Vibrionales: 0.89       Vibrionaceae: 0.89      Vibrio: 0.89    Vibrio cholerae: 0.69
+  genome3.fna     classified      based on 4/9 ORFs       1;131567;2;1783272;1239;91061;1385;186820;1637;1639     1.00;1.00;1.00;0.76;0.76;0.76;0.76;0.76;0.76;0.76       Bacteria: 1.00  Firmicutes: 0.76        Bacilli: 0.76   Bacillales: 0.76        Listeriaceae: 0.76      Listeria: 0.76  Listeria monocytogenes: 0.76
+
+
+**OUTPUT**
+
+::
+
+  # total number of bins is 2, of which 2 (100.00%) are classified.
+  #
+  # rank  clade   number of bins
+  superkingdom    Bacteria        2
+  phylum  Proteobacteria  1
+  phylum  Firmicutes      1
+  class   Gammaproteobacteria     1
+  class   Bacilli 1
+  order   Vibrionales     1
+  order   Bacillales      1
+  family  Vibrionaceae    1
+  family  Listeriaceae    1
+  genus   Vibrio  1
+  genus   Listeria        1
+  species Vibrio cholerae 1
+  species Listeria monocytogenes  1
+
+
+Required arguments:
+  -i, --input_file     Path to named CAT contig classification file or BAT
+                       bin classification file. Currently only official ranks
+                       are supported, and only classification files
+                       containing a single classification per contig / bin.
+
+Optional arguments:
+  -c, --contigs_fasta
+                        Path to contigs fasta file. This is required if you
+                        want to summarise a contig classification file.
+
+@COMMON_HELP@
+    ]]></help>
+    <expand macro="citations" />
+</tool>