diff fastani.xml @ 0:93549392d20d draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastani commit 6410237f37dfd76382f9780e73a14cf48aba3695-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastani.xml	Fri Jul 19 06:49:02 2019 -0400
@@ -0,0 +1,62 @@
+<tool id="fastani" name="FastANI" version="1.1">
+    <description> fast alignment-free computation of whole-genome Average Nucleotide Identity</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <version_command>fastANI --version</version_command>
+    <command detect_errors="exit_code">
+    <![CDATA[
+    #for $counter_q, $input_q in enumerate($query):
+        ln -fs '$input_q' ${input_q.element_identifier}_query &&
+        echo ${input_q.element_identifier}_query >> query.lst &&
+    #end for
+
+    #for $counter_r, $input_r in enumerate($reference):
+        ln -fs '$input_r' ${input_r.element_identifier}_ref &&
+        echo ${input_r.element_identifier}_query >> ref.lst &&
+    #end for
+    
+    fastANI 
+    #if len($query) == 1 and len($reference) == 1:
+        -q ${input_q.element_identifier}_query -r  ${input_r.element_identifier}_ref -o output
+    #elif len($query) == 1 and len($reference) > 1:
+        -q ${input_q.element_identifier}_query --rl ref.lst  -o output
+    #elif len($query) > 1 and len($reference) > 1:
+        --ql query.lst --rl ref.lst -o output
+    #end if
+    
+    2>&1
+    ]]></command>
+    <inputs>
+        <param name="query" type="data" format="fasta" multiple="true" label="Query sequences" />
+        <param name="reference" type="data" format="fasta" multiple="true" label="Reference sequence" />
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" from_work_dir="output" label="${tool.name} on ${on_string} Output"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="query" value="Shigella_flexneri_2a_01.fna" />
+            <param name="reference" value="Escherichia_coli_str_K12_MG1655.fna" />
+            <output name="output" file="fastani.out" compare="sim_size" />
+        </test>
+    </tests>
+    <help><![CDATA[
+    FastANI is developed for fast alignment-free computation of whole-genome
+    Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide
+    identity of orthologous gene pairs shared between two microbial genomes.
+    FastANI supports pairwise comparison of both complete and draft genome
+    assemblies. Its underlying procedure follows a similar workflow as described
+    by Goris et al. 2007. However, it avoids expensive sequence alignments and
+    uses Mashmap as its MinHash based sequence mapping engine to compute the
+    orthologous mappings and alignment identity estimates. Based on our
+    experiments with complete and draft genomes, its accuracy is on par with
+    BLAST-based ANI solver and it achieves two to three orders of magnitude
+    speedup. Therefore, it is useful for pairwise ANI computation of large
+    number of genome pairs. More details about its speed, accuracy and potential
+    applications are described here: "High Throughput ANI Analysis of 90K
+    Prokaryotic Genomes Reveals Clear Species Boundaries".
+    ]]></help>
+    <expand macro="citations" />
+</tool>