diff freyja_boot.xml @ 0:dda5772507b2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/freyja_boot.xml	Thu Jul 28 09:25:33 2022 +0000
@@ -0,0 +1,122 @@
+<tool id="freyja_boot" name="Freyja: Bootstrapping" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
+      profile="@PROFILE@">
+    <description>
+        method
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="biotools"/>
+    <expand macro="requirements"/>
+    <expand macro="version"/>
+    <command detect_errors="exit_code"><![CDATA[
+@RUN_FREYJA_UPDATE_COMMAND@
+@PREPROCESS_VCF_INPUT@
+freyja boot
+    @STANDARD_INPUT_FOR_BOOT@
+    --nt \${GALAXY_SLOTS:-4}
+    #if $nb
+        --nb $nb
+    #end if
+    --output_base 'boot_output'
+    @CUSTOM_BARCODES_COMMAND@
+    $boxplot_pdf
+    ]]></command>
+    <inputs>
+        <param name="variants_file" type="data" format="tabular" label="Variants file"/>
+        <expand macro="demixing_common_options"/>
+        <param argument="--nb" type="integer" optional="true" label="Number of bootstraps"/>
+        <param name="boxplot_pdf" argument="--boxplot pdf" type="boolean" truevalue="--boxplot pdf"
+               falsevalue=""
+               checked="false" label="Generate boxplot"/>
+    </inputs>
+    <outputs>
+        <data name="boot_lineages" format="csv" label="${tool.name} on ${on_string}: Lineages"
+              from_work_dir="boot_output_lineages.csv"/>
+        <data name="boot_summarized" format="csv" label="${tool.name} on ${on_string}: Summarized"
+              from_work_dir="boot_output_summarized.csv">
+        </data>
+        <data name="boot_lineages_plot" format="pdf"
+              label="${tool.name} on ${on_string}: Lineages boxplot"
+              from_work_dir="boot_output_lineages.pdf">
+            <filter>boxplot_pdf</filter>
+        </data>
+        <data name="boot_summarized_plot" format="pdf"
+              label="${tool.name} on ${on_string}: Summarized boxplot"
+              from_work_dir="boot_output_summarized.pdf">
+            <filter>boxplot_pdf</filter>
+        </data>
+    </outputs>
+    <tests>
+        <!-- Test 01: test tsv input files and plots -->
+        <test expect_num_outputs="4">
+            <conditional name="usher_update_option">
+                <param name="choice" value="repo"/>
+            </conditional>
+            <param name="variants_file" value="variants.tsv"/>
+            <param name="depth_file" value="depths.tsv"/>
+            <param name="confirmedonly" value="false"/>
+            <param name="nb" value="10"/>
+            <param name="boxplot_pdf" value="true"/>
+            <output name="boot_lineages" ftype="csv">
+                <assert_contents>
+                    <has_text text="B.1.617.2"/>
+                </assert_contents>
+            </output>
+            <output name="boot_summarized" ftype="csv">
+                <assert_contents>
+                    <has_text text="Delta"/>
+                </assert_contents>
+            </output>
+            <output name="boot_lineages_plot" ftype="pdf">
+                <assert_contents>
+                    <has_text text="Matplotlib"/>
+                </assert_contents>
+            </output>
+            <output name="boot_summarized_plot" ftype="pdf">
+                <assert_contents>
+                    <has_text text="Matplotlib"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test 02: test VCF input file -->
+        <test expect_num_outputs="2">
+            <conditional name="usher_update_option">
+                <param name="choice" value="repo"/>
+            </conditional>
+            <param name="variants_file" value="test.vcf"/>
+            <param name="depth_file" value="depths.tsv"/>
+            <param name="confirmedonly" value="false"/>
+            <param name="nb" value="10"/>
+            <param name="boxplot_pdf" value="false"/>
+            <output name="boot_lineages" ftype="csv">
+                <assert_contents>
+                    <has_text text="B.1.617.2"/>
+                </assert_contents>
+            </output>
+            <output name="boot_summarized" ftype="csv">
+                <assert_contents>
+                    <has_text text="Delta"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_HEADER@
+
+Information about **freyja boot** method
+========================================
+
+A fast bootstrapping method for freyja.
+
+Outputs
+=======
+
+Bootstrapping method results:
+
+1. Bootstrap lineages: the 0.025, 0.05,0.25,0.5 (median),0.75, 0.95, and 0.975 percentiles for each lineage;
+2. Bootstrap summarized: WHO designated VOI/VOC
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>