diff hal_halCoverage.xml @ 0:48d453b8f39d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/haltools commit 6244b9d15a5ad97ae20191e2f8fbafe2050c3cac

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hal_halCoverage.xml	Fri Feb 06 10:39:17 2026 +0000
@@ -0,0 +1,83 @@
+<tool id="hal_halcoverage" name="halCoverage" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>calculates coverage by sampling bases</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/> 
+    <expand macro="stdio"/>
+    <command detect_errors="aggressive"><![CDATA[
+        set -o pipefail; ## Sets the pipeline’s exit code to halCoverage’s on failure.
+        halCoverage
+            --numSamples $numSamples
+            --seed $seed
+            $bySequence
+            ## Pipes output to replace commas with tabs. Output is mostly numerical, and Genome names contain no commas, as this would invalidate the HAL Newick tree.
+            '$input_hal' '$refGenome' | tr ',' '\t' > '$out_file' 
+    ]]></command>
+    <inputs>
+        <expand macro="input_hal"/>
+        <expand macro="params_refGenome"/>
+        <expand macro="params_numSamples"/>
+        <expand macro="params_seed"/>
+        <param argument="--bySequence" type="boolean" truevalue="--bySequence" falsevalue="" checked="false" label="Coverage breakdown by sequence" help="Provide coverage breakdown by sequence in reference genome"/>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="tabular" label="${tool.name} on ${on_string}: ${refGenome}"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_hal" value="halTest.hal"/>
+            <param name="refGenome" value="Genome_1"/>
+            <param name="seed" value="100"/>
+            <output name="out_file" ftype="tabular">
+                <assert_contents>
+                    <has_line line="Genome&#009; sitesCovered1Times&#009; sitesCovered2Times&#009; sitesCovered3Times&#009; sitesCovered4Times&#009; sitesCovered5Times"/>
+                    <has_line line="Genome_2&#009; 856475&#009; 482343&#009; 482343&#009; 214021&#009; 0"/>
+                    <has_n_lines n="4"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_hal" value="halTest.hal"/>
+            <param name="refGenome" value="Genome_1"/>
+            <param name="numSamples" value="1000"/>
+            <param name="seed" value="100"/>
+            <output name="out_file" ftype="tabular">
+                <assert_contents>
+                    <has_line line="Genome&#009; sitesCovered1Times&#009; sitesCovered2Times&#009; sitesCovered3Times&#009; sitesCovered4Times&#009; sitesCovered5Times"/>
+                    <has_line line="Genome_2&#009; 839&#009; 500&#009; 500&#009; 233&#009; 0"/>
+                    <has_n_lines n="4"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_hal" value="halTest.hal"/>
+            <param name="refGenome" value="Genome_1"/>
+            <param name="bySequence" value="true"/>
+            <param name="seed" value="100"/>
+            <output name="out_file" ftype="tabular">
+                <assert_contents>
+                    <has_line line="Genome&#009; sitesCovered1Times&#009; sitesCovered2Times&#009; sitesCovered3Times&#009; sitesCovered4Times&#009; sitesCovered5Times"/>
+                    <has_line line="Genome_2&#009; 856475&#009; 482343&#009; 482343&#009; 214021&#009; 0"/>
+                    <has_line line="Coverage on Genome_1_seq"/>
+                    <has_n_lines n="9"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+halCoverage estimates how well a reference genome is represented in a HAL alignment by randomly sampling bases. 
+It takes a HAL file and a reference genome name as input and outputs a table summarizing the result. 
+A random seed can be adjusted for reproducibility.
+
+Use it for assessing alignment completeness and identifying underrepresented regions in a genome alignment.
+
+-----
+
+.. class:: warningmark
+
+Running the tool on a HAL file in mmap format may fail or run infinite if 'Coverage breakdown by sequence' is enabled, while the HDF5 format can run successfully. It is recommended to convert the input to HDF5 format first using halExtract.
+    ]]></help>
+    <expand macro="citation"/>
+    <expand macro="creator"/>
+</tool>
\ No newline at end of file