# HG changeset patch
# User iuc
# Date 1710258133 0
# Node ID 61a6b93ee6e10941ad63ce3b6b1c629a81dd9ad9

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit cd34bba7aafb92ea993d4ef17a3669957de7c537

diff -r 000000000000 -r 61a6b93ee6e1 bam2fastx.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bam2fastx.xml	Tue Mar 12 15:42:13 2024 +0000
@@ -0,0 +1,77 @@
+<tool id="bam2fastx" name="PacBio bam2fastx" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
+    <description>PacBio BAM to Fastx</description>
+    <macros>
+        <token name="@TOOL_VERSION@">3.1.1</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">pbtk</requirement>
+    </requirements>
+    <command><![CDATA[
+mkdir -p output_files/ &&
+ln -s '$input_bam' input.bam &&
+pbindex input.bam &&
+#if $output_format == "fasta_gz":
+    bam2fasta -o output
+#elif $output_format == "fastq_gz":
+    bam2fastq -o output
+#end if
+input.bam
+--num-threads  "\${GALAXY_SLOTS:-1}"  &&
+#if $output_format == "fasta":
+    mv output.fasta.gz '$output_fasta_gz'
+#elif $output_format == "fastq":
+    mv output.fastq.gz '$output_fastq_gz'
+#end if
+    ]]></command>
+    <inputs>
+        <param name="input_bam" type="data" format="unsorted.bam" label="PacBio Bam file "/>
+        <param name="output_format" type="select" label="Output Format" help="Output a fasta.gz or fastq.gz">
+            <option value="fastq_gz">fastq.gz</option>
+            <option value="fasta_gz">fasta.gz</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output_fasta_gz" format="fasta.gz" label="${tool.name} on ${on_string}: Fasta">
+            <filter>output_format == "fasta"</filter>
+        </data>
+        <data name="output_fastq_gz" format="fastqsanger.gz" label="${tool.name} on ${on_string}: Fastq">
+            <filter>output_format == "fastq"</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_bam" ftype="unsorted.bam" value="sample.bam"/>
+            <param name="output_format" value="fastq_gz" />
+            <output name="output_fastq_gz">
+                <assert_contents>
+                    <has_size min="9000" />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1" >
+            <param name="input_bam" ftype="bam" value="sample.bam"/>
+            <param name="output_format" value="fasta_gz" />
+            <output name="output_fasta_gz" >
+                <assert_contents>
+                    <has_size min="9000" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+Convert a PacBio BAM file to Fastq or Fasta file.
+    ]]></help>
+        <citations>
+            <citation type="bibtex">
+                @misc{githubpbtk,
+                author = {},
+                year = {2024},
+                title = {pbtk},
+                publisher = {GitHub},
+                journal = {GitHub repository},
+                url = {https://github.com/PacificBiosciences/pbtk},
+                }
+            </citation>
+        </citations>
+ </tool>
diff -r 000000000000 -r 61a6b93ee6e1 test-data/sample.bam
Binary file test-data/sample.bam has changed