adding HalfDeep

tools/halfdeep/.shed.yml

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+categories:
+- Sequence Analysis
+description: "HalfDeep: Automated detection of intervals covered at half depth by sequenced reads."
+homepage_url: https://github.com/makovalab-psu/HalfDeep
+long_description: |
+    Automated detection of intervals covered at half depth by sequenced reads.
+name: halfdeep
+owner: iuc
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/halfdeep
+type: unrestricted

tools/halfdeep/halfdeep.xml

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+<tool id="halfdeep" name="HalfDeep" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Automated detection of intervals covered at half depth by sequenced reads.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        #import os
+        ##
+        ## reference
+        ##
+        reference_filename="ref.fasta" &&
+        if [ "\$(head -c 2 '$ref' | xxd -p)" = "1f8b" ]; then reference_filename="ref.fasta.gz"; fi &&
+        ln -s '$ref' "\$reference_filename" &&
+        touch ref.idx &&
+        ##
+        ## reads
+        ##
+        #set $reads_dir = "reads"
+        #set $mapped_reads_dir = "halfdeep/ref/mapped_reads"
+        mkdir -p '$reads_dir' '$mapped_reads_dir' &&
+        #for $read in $reads
+            #set $seq_base = os.path.basename(str($read))
+            ln -s '$read' '$reads_dir/$seq_base' &&
+            echo '$reads_dir/$seq_base' >> input.fofn &&
+            ##
+            ## mapped reads
+            ##
+            #for $mapped_read in $mapped_reads
+                ln -s '$mapped_read' "$mapped_reads_dir/${seq_base}.bam" &&
+                ln -s "${seq_base}.bam" "$mapped_reads_dir/${seq_base}.sort.bam" &&
+                ln -s '$mapped_read.metadata.bam_index' "$mapped_reads_dir/${seq_base}.sort.bam.bai" &&
+            #end for
+        #end for
+        ##
+        ## run bam_depth.sh
+        ##
+        #for $line_number in range(1, len($reads) + 1)
+            bam_depth.sh "\$reference_filename" $line_number &&
+        #end for
+        ##
+        ## run halfdeep.sh
+        ##
+        halfdeep.sh "\$reference_filename"
+    ]]></command>
+    <inputs>
+        <param name="ref" type="data" format="fasta,fasta.gz" label="Genome Assembly" help="A Genome Assembly in FASTA format."/>
+        <param name="reads" type="data" format="fastqsanger,fastqsanger.gz" multiple="true" label="Sequencing Reads" help="Sequencing Reads for the Genome Assembly in FASTQ format."/>
+        <param name="mapped_reads" type="data" format="bam" multiple="true" label="Aligned Reads" help="Alignments of the Sequencing Reads to the Genome Assembly in BAM format."/>
+    </inputs>
+    <outputs>
+        <data name="scaffold_len" format="tabular" from_work_dir="halfdeep/ref/scaffold_lengths.dat" label="Scaffold lengths for ${on_string}"/>
+        <data name="depth_dat" format="tabular.gz" from_work_dir="halfdeep/ref/depth.dat.gz" label="Depth for ${on_string}"/>
+        <data name="pct_cmds" format="text" from_work_dir="halfdeep/ref/percentile_commands.sh" label="Percentile to value for ${on_string}"/>
+        <data name="halfdeep_dat" format="tabular" from_work_dir="halfdeep/ref/halfdeep.dat" label="HalfDeep on ${on_string}"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="4">
+            <param name="ref" value="ref.fasta.gz" ftype="fasta.gz"/>
+            <param name="reads" value="reads.fasta.gz" ftype="fasta.gz"/>
+            <param name="mapped_reads" value="mapped_reads.bam" ftype="bam"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+Inputs are an assembly in FASTA format, reads in FASTQ format, and mapped reads in BAM format.
+
+The final output is a halfdeep.dat file. This is a list of intervals (origin 1, closed) that the process has called as 'covered at half depth'.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>

tools/halfdeep/macros.xml

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+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">halfdeep</requirement>
+        </requirements>
+    </xml>
+    <token name="@TOOL_VERSION@">0.1.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">21.05</token>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @misc{github_halfdeep,
+                    author = {Makova Lab PSU},
+                    year = "2019",
+                    title = {HalfDeep},
+                    publisher = {GitHub},
+                    journal = {GitHub repository},
+                    url = {https://github.com/makovalab-psu/HalfDeep}
+            </citation>
+        </citations>
+    </xml>
+</macros>