diff preseq_lc_extrap.xml @ 0:079f2ee9bd64 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/preseq commit 730a243f12a30a36277b58fb0d92891c81af4c6f

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/preseq_lc_extrap.xml	Wed Mar 11 19:19:04 2026 +0000
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+<tool id="preseq_lc_extrap" name="Preseq lc_extrap" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Yield Extrapolation</description>
+    
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+
+    <command detect_errors="exit_code"><![CDATA[
+        ## 1. File Preparation: Symlink the input BAM to a standard name
+		ln -s '$input_bam' input.bam &&
+        
+		## 2. lc_extrap Analysis Execute
+        preseq lc_extrap 
+            -B input.bam
+            $verbose
+            -e $extrap_limit
+            -s $step_size
+            -o '$output_tsv' 
+    ]]></command>
+
+    <inputs>
+        <expand macro="macro_input_bam" />
+        <param argument="-e" name="extrap_limit" type="integer" value="10000000" label="Extrapolation Limit" help="Total number of reads to extrapolate to."/>
+        <param argument="-s" name="step_size" type="integer" value="100000" label="Step Size" help="Step size for extrapolation."/>
+        <expand macro="macro_verbose" />
+    </inputs>
+
+    <outputs>
+        <data name="output_tsv" format="tsv"/>
+    </outputs>
+
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_bam" value="test.bam" ftype="bam"/>
+            <param name="extrap_limit" value="100000"/>
+            <param name="step_size" value="10000"/>
+            <output name="output_tsv" file="test_lc_extrap.tsv" ftype="tsv" lines_diff="4"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+**Preseq: lc_extrap**
+
+The `lc_extrap` tool from the Preseq package predicts the expected yield of distinct reads for future sequencing efforts. By analyzing the current complexity of a genomic library, it calculates an extrapolation curve. This helps answer the question: "If I sequence this library deeper, how many new, unique reads will I discover?"
+
+**Input**
+
+- A **coordinate-sorted** BAM file containing aligned reads.
+
+**Output**
+
+- A tabular (TSV) file containing the extrapolated yield curve. This file is suitable for plotting and can be integrated into MultiQC reports.
+    ]]></help>
+    
+    <expand macro="citations"/>
+
+</tool>