# HG changeset patch
# User iuc
# Date 1720630876 0
# Node ID add156116c63c03394c8398c5d64756549db8139
# Parent  c8f1cd6c1fbfc1b81092e31b9a70b1dd34f92221
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072

diff -r c8f1cd6c1fbf -r add156116c63 rasusa.xml
--- a/rasusa.xml	Wed Feb 28 15:16:59 2024 +0000
+++ b/rasusa.xml	Wed Jul 10 17:01:16 2024 +0000
@@ -1,7 +1,7 @@
 <tool id="rasusa" name="rasusa" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
     <description>Randomly subsample reads to a specified coverage</description>
     <macros>
-        <token name="@TOOL_VERSION@">0.8.0</token>
+        <token name="@TOOL_VERSION@">2.0.0</token>
         <token name="@VERSION_SUFFIX@">0</token>
         <token name="@FORMATS@">fastqsanger,fastqsanger.gz,fasta,fasta.gz</token>
         <xml name="size_units">
@@ -11,35 +11,36 @@
             <option value="g">Giga bases</option>
             <option value="t">Tera bases</option>
         </xml>
-    </macros>
-    <xrefs>
-        <xref type='bio.tools'>rasusa</xref>
-    </xrefs>
-    <requirements>
-        <requirement type="package" version="@TOOL_VERSION@">rasusa</requirement>
-    </requirements>
-
-    <command detect_errors="exit_code"><![CDATA[
-rasusa
-#if str( $input.input_selector ) == "paired":
-    #set r1_ext = $input.reads1.extension
-    #set r2_ext = $input.reads2.extension
--i '${input.reads1}'
--i '${input.reads2}'
--o 'paired_out1.$r1_ext'
--o 'paired_out2.$r2_ext'
-#elif str( $input.input_selector ) == "paired_collection":
-    #set r1_ext = $input.collection.forward.extension
-    #set r2_ext = $input.collection.reverse.extension
--i '${input.collection.forward}'
--i '${input.collection.reverse}'
--o 'paired_out1.$r1_ext'
--o 'paired_out2.$r2_ext'
-#else:
-    #set r1_ext = $input.reads.extension
--i '${input.reads}'
--o 'single_out.$r1_ext'
-#end if
+        <xml name="params_fastq">
+            <conditional name="subsample">
+                <param name="type" type="select" label="Subsample reads based on">
+                    <option value="coverage">Coverage</option>
+                    <option value="num_bases">Number of bases</option>
+                    <option value="num_reads">Number of reads</option>
+                    <option value="frac_reads" selected="true">Fraction of reads</option>
+                </param>
+                <when value="coverage">
+                    <param name="genome_size_unit" type="select" label="Specify genome size in">
+                        <expand macro="size_units" />
+                    </param>
+                    <param name="genome_size" type="float" min="0" value="" label="Genome size to calculate coverage with respect to"/>
+                    <param argument="--coverage" type="float" min="0" value="" label="The desired coverage to subsample the reads to"/>
+                </when>
+                <when value="num_bases">
+                    <param name="num_bases_unit" type="select" label="Specify number of bases in">
+                        <expand macro="size_units" />
+                    </param>
+                    <param name="bases" type="float" min="0" value="" label="Explicitly set the number of bases required"/>
+                </when>
+                <when value="num_reads">
+                    <param argument="--num" type="integer" value="" min="1"/>
+                </when>
+                <when value="frac_reads">
+                    <param argument="--frac" type="float" value="0.1" min="0" max="1"/>
+                </when>
+            </conditional>
+        </xml>
+        <token name="@FASTQ_SUBSAMPLE_OPTIONS@"><![CDATA[
 #if str( $subsample.type ) == "coverage":
 --genome-size '$subsample.genome_size$subsample.genome_size_unit'
 --coverage $subsample.coverage
@@ -50,68 +51,96 @@
 #elif str( $subsample.type ) == "frac_reads":
 --frac $subsample.frac
 #end if
--s $seed
 #if $r1_ext.endswith(".gz") or $r2_ext.endswith(".gz")
 --output-type g
+#end if    ]]>
+    </token>
+    </macros>
+    <xrefs>
+        <xref type='bio.tools'>rasusa</xref>
+    </xrefs>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">rasusa</requirement>
+        <requirement type="package" version="1.20">samtools</requirement>
+    </requirements>
+
+    <command detect_errors="exit_code"><![CDATA[
+#if str( $input.input_selector ) == "aligned":
+ln -s '$bam' 'input.bam' &&
+ln -s '$bam.metadata.bam_index' 'input.bam.bai' &&
+rasusa aln
+--coverage $input.coverage
+--step-size $input.step_size
+#else:
+rasusa reads
 #end if
-&&
+
+#if $seed
+-s $seed
+#end if
 
 #if str( $input.input_selector ) == "paired":
+    #set r1_ext = $input.reads1.extension
+    #set r2_ext = $input.reads2.extension
+-o 'paired_out1.$r1_ext'
+-o 'paired_out2.$r2_ext'
+@FASTQ_SUBSAMPLE_OPTIONS@
+'${input.reads1}'
+'${input.reads2}' &&
 mv 'paired_out1.$r1_ext' '$paired_output1' &&
 mv 'paired_out2.$r2_ext' '$paired_output2'
+
 #elif str( $input.input_selector ) == "paired_collection":
+    #set r1_ext = $input.collection.forward.extension
+    #set r2_ext = $input.collection.reverse.extension
+-o 'paired_out1.$r1_ext'
+-o 'paired_out2.$r2_ext'
+@FASTQ_SUBSAMPLE_OPTIONS@
+'${input.collection.forward}'
+'${input.collection.reverse}' &&
 mv 'paired_out1.$r1_ext' '${collection_output.forward}' &&
 mv 'paired_out2.$r2_ext' '${collection_output.reverse}'
-#else:
+
+#elif str( $input.input_selector ) == "single":
+    #set r1_ext = $input.reads.extension
+-o 'single_out.$r1_ext'
+@FASTQ_SUBSAMPLE_OPTIONS@
+'${input.reads}' &&
 mv 'single_out.$r1_ext' '$single_output'
+
+#elif str( $input.input_selector ) == "aligned":
+'input.bam' | samtools sort --no-PG -@ 1 -T '\${TMPDIR:-.}' -O bam -o '$bam_output' -
 #end if
     ]]></command>
     <inputs>
         <conditional name="input">
             <param name="input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
-                <option value="paired">Paired</option>
-                <option value="single">Single</option>
-                <option value="paired_collection">Paired Collection</option>
+                <option value="paired">Paired-end FASTQ</option>
+                <option value="single">Single-end FASTQ</option>
+                <option value="paired_collection">Paired FASTQ Collection</option>
+                <option value="aligned">BAM file of aligned reads</option>
             </param>
             <when value="paired">
                 <param name="reads1" type="data" format="@FORMATS@" label="Select first set of reads" help="Specify dataset with forward reads"/>
                 <param name="reads2" type="data" format="@FORMATS@" label="Select second set of reads" help="Specify dataset with reverse reads"/>
+                <expand macro="params_fastq" />
             </when>
             <when value="single">
                 <param name="reads" type="data" format="@FORMATS@" label="Select fasta/fastq dataset" help="Specify dataset with single reads"/>
+                <expand macro="params_fastq" />
             </when>
             <when value="paired_collection">
                 <param name="collection" format="@FORMATS@" type="data_collection" collection_type="paired" label="Select a paired collection"/>
+                <expand macro="params_fastq" />
+            </when>
+            <when value="aligned">
+                <param name="bam" format="sam,bam" type="data" label="Select BAM file(s) with alignments"/>
+                <param argument="--coverage" type="integer" min="0" optional="true" value="" label="The desired depth of coverage to subsample the alignment to"/>
+                <param type="integer" argument="--step-size" value="100" label="When a region has less than the desired coverage, the step size to move along the chromosome to find more reads."
+                    help="The lowest of the step and the minimum end coordinate of the reads in the region will be used. This parameter can have a significant impact on the runtime of the subsampling process."/>
             </when>
         </conditional>
-        <conditional name="subsample">
-            <param name="type" type="select" label="Subsample reads based on">
-                <option value="coverage">Coverage</option>
-                <option value="num_bases">Number of bases</option>
-                <option value="num_reads">Number of reads</option>
-                <option value="frac_reads" selected="true">Fraction of reads</option>
-            </param>
-            <when value="coverage">
-                <param name="genome_size_unit" type="select" label="Specify genome size in">
-                    <expand macro="size_units" />
-                </param>
-                <param name="genome_size" type="float" min="0" value="" label="Genome size to calculate coverage with respect to"/>
-                <param argument="--coverage" type="float" min="0" value="" label="The desired coverage to sub-sample the reads to"/>
-            </when>
-            <when value="num_bases">
-                <param name="num_bases_unit" type="select" label="Specify number of bases in">
-                    <expand macro="size_units" />
-                </param>
-                <param name="bases" type="float" min="0" value="" label="Explicitly set the number of bases required"/>
-            </when>
-            <when value="num_reads">
-                <param argument="--num" type="integer" value="" min="1"/>
-            </when>
-            <when value="frac_reads">
-                <param argument="--frac" type="float" value="0.1" min="0" max="1"/>
-            </when>
-        </conditional>
-        <param type="integer" name="seed" optional="true" label="Random seed to use"/>
+        <param type="integer" argument="--seed" optional="true" label="Random seed to use"/>
     </inputs>
     <outputs>
         <data name="paired_output1" label="${tool.name} on ${on_string}: paired-end r1" format_source="reads1">
@@ -128,6 +157,9 @@
             <data name="forward" label="${tool.name} on ${input.collection.forward.name}: paired-end r1" format_source="collection['forward']"/>
             <data name="reverse" label="${tool.name} on ${input.collection.reverse.name}: paired-end R2" format_source="collection['reverse']"/>
         </collection>
+        <data name="bam_output" label="${tool.name} on ${on_string}: BAM" format="bam">
+            <filter>input['input_selector'] == 'aligned'</filter>
+        </data>
     </outputs>
     <tests>
         <test expect_num_outputs="1">
@@ -163,7 +195,7 @@
             <output name="paired_output2" value="paired2_by_coverage_k.fastq.gz" ftype="fastqsanger.gz"/>
         </test>
         <test expect_num_outputs="3">
-            <!-- test 3: paired-collection fastq by coverage in mb-->
+            <!-- test 3: paired-collection fastq by coverage in mb -->
             <conditional name="input">
                 <param name="input_selector" value="paired_collection"/>
                 <param name="collection">
@@ -232,7 +264,7 @@
             <output name="paired_output2" value="paired2_by_num_reads.fasta.gz" ftype="fasta.gz"/>
         </test>
         <test expect_num_outputs="3">
-            <!-- test 7: paired-collection fasta by fraction reads-->
+            <!-- test 7: paired-collection fasta by fraction reads -->
             <conditional name="input">
                 <param name="input_selector" value="paired_collection"/>
                 <param name="collection">
@@ -252,6 +284,16 @@
                 <element name="reverse" file="paired2_by_frac_reads.fasta" ftype="fasta"/>
             </output_collection>
         </test>
+        <test expect_num_outputs="1">
+            <!-- test 8: bam input -->
+            <conditional name="input">
+                <param name="input_selector" value="aligned"/>
+                <param name="bam" value="input.bam" />
+            </conditional>
+            <param name="coverage" value="1"/>
+            <param name="seed" value="1"/>
+            <output name="bam_output" value="output.bam" ftype="bam"/>
+        </test>
     </tests>
     <help><![CDATA[
 
diff -r c8f1cd6c1fbf -r add156116c63 test-data/input.bam
Binary file test-data/input.bam has changed
diff -r c8f1cd6c1fbf -r add156116c63 test-data/output.bam
Binary file test-data/output.bam has changed