diff funannotate_compare.xml @ 0:857f7ac611e1 draft

"planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/funannotate_compare.xml	Mon Oct 04 19:38:37 2021 +0000
@@ -0,0 +1,124 @@
+<tool id="funannotate_compare" name="Funannotate compare" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+    <description>annotations</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <expand macro="requirements" />
+    </requirements>
+    <version_command>funannotate check --show-versions</version_command>
+    <command><![CDATA[
+#set $inputs = ""
+#for i, f in enumerate($input):
+    #set $inputs = $inputs + " input" + str($i) + ".gbk"
+    ln -s '$f' input${i}.gbk &&
+#end for
+
+funannotate compare
+--input
+
+$inputs
+
+--out output
+
+--database '$database.fields.path'
+
+#if $run_dnds in ['estimate', 'full']:
+    --run_dnds ${run_dnds}
+#end if
+
+## TODO add --outgroup option some day (hard to get an up to date/customizable list)
+
+--go_fdr ${go_fdr}
+
+--heatmap_stdev ${heatmap_stdev}
+
+--num_orthos ${num_orthos}
+
+#if $proteinortho:
+    --proteinortho '${proteinortho}'
+#end if
+
+--ml_method ${ml.ml_method}
+
+#if $ml.ml_method == 'raxml':
+    --bootstrap '${ml.bootstrap}'
+#end if
+
+--cpus \${GALAXY_SLOTS:-2}
+
+&&
+
+mkdir -p '$output.files_path' &&
+cp -R output/* '$output.files_path' &&
+cp output/index.html '$output'
+    ]]></command>
+    <inputs>
+        <param argument="--input" type="data" format="genbank" multiple="true" label="Genome annotations in genbank format" help="Outputs from 'Funannotate predict annotation' tool" />
+
+        <param name="database" label="Funannotate database" type="select">
+            <options from_data_table="funannotate">
+                <column name="value" index="0" />
+                <column name="name" index="1" />
+                <column name="path" index="3" />
+                <filter type="sort_by" column="0" />
+                <filter type="static_value" column="2" value="1.0" />
+            </options>
+        </param>
+
+        <param argument="--run_dnds" type="select" label="Calculate dN/dS ratio on all orthologs">
+            <option value="no" selected="True">No</option>
+            <option value="estimate">estimate</option>
+            <option value="full">full</option>
+        </param>
+
+        <param argument="--go_fdr" type="float" value="0.05" label="P-value for FDR GO-enrichment" />
+        <param argument="--heatmap_stdev" type="float" value="1.0" label="Cut-off for heatmap" />
+        <param argument="--num_orthos" type="integer" value="500" label="Number of Single-copy orthologs to use for ML" />
+        <param argument="--proteinortho" type="data" format="tabular" optional="true" label="Proteinortho POFF results" help="TSV format, if available"/>
+
+        <conditional name="ml">
+            <param argument="--ml_method" type="select" label="Maximum Likelihood method">
+                <option value="iqtree" selected="True">iqtree</option>
+                <option value="raxml">raxml</option>
+            </param>
+            <when value="iqtree" />
+            <when value="raxml">
+                <param argument="--bootstrap" type="integer" value="100" label="Number of boostrap replicates to run with RAxML" />
+            </when>
+        </conditional>
+
+        <!-- Need this to change path in the test funannotate_db -->
+        <param type="hidden" name="uglyTestingHack" value="" />
+    </inputs>
+    <outputs>
+        <data name='output' format='html' label="${tool.name} on ${on_string}: report" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="compare/Genus_species.gbk,compare/Other_species.gbk,compare/Other_beast.gbk,compare/Yet_another.gbk" />
+            <param name="database" value="2021-07-20-120000" />
+            <param name="outputs" value="gbk" />
+            <conditional name="ml">
+                <param name="ml_method" value="raxml" />
+            </conditional>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="Report generated on:" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+Funannotate_ compare
+--------------------
+
+Funannotate_ is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).
+
+This script does light-weight comparative genomics between funannotated genomes.  Output
+is graphs, phylogeny, CSV files, etc --> visualized in web-browser.
+
+.. _Funannotate: http://funannotate.readthedocs.io
+    ]]></help>
+    <expand macro="citations" />
+</tool>