diff hisat2.xml @ 31:f4af63aaf57a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03

--- a/hisat2.xml	Sun Jul 18 17:50:55 2021 +0000
+++ b/hisat2.xml	Wed Jul 06 10:26:44 2022 +0000
@@ -3,6 +3,9 @@
     <macros>
         <import>hisat2_macros.xml</import>
     </macros>
+    <xrefs>
+        <xref type="bio.tools">hisat2</xref>
+    </xrefs>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">hisat2</requirement>
         <requirement type="package" version="1.12">samtools</requirement>
@@ -561,8 +564,8 @@
                     <param name="no_unal" argument="--no-unal" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppress SAM records for reads that failed to align." help="Default: false"/>
                     <conditional name="read_groups">
                         <param name="rg_labels" type="select" label="Edit Read Group IDs">
-                            <option value="No" />
-                            <option value="Yes" />
+                            <option value="No">No</option>
+                            <option value="Yes">Yes</option>
                         </param>
                         <when value="No"/>
                         <when value="Yes">
@@ -758,7 +761,9 @@
             <param name="input_2" ftype="fastqsanger" value="hisat_input_1_reverse.fastq" />
             <param name="adv|reporting_options|reporting_options_selector" value="advanced"/>
             <param name="novel_splicesite_outfile" value="false" />
-            <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" />
+            <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" >
+                <metadata name="sort_order" value="coordinate"/>
+            </output>
         </test>
         <!-- Ensure advanced scoring options work -->
         <test expect_num_outputs="1" >
@@ -768,7 +773,9 @@
             <param name="input_1" ftype="fastqsanger" value="hisat_input_1_forward.fastq" />
             <param name="input_2" ftype="fastqsanger" value="hisat_input_1_reverse.fastq" />
             <param name="adv|scoring_options|coefficient" value="-0.3"/>
-            <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" />
+            <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" sort="true" >
+                <metadata name="sort_order" value="coordinate"/>
+            </output>
         </test>
         <!-- Ensure built-in reference works -->
         <test expect_num_outputs="1">
@@ -776,7 +783,9 @@
             <param name="source" value="indexed" />
             <param name="input_1" ftype="fastqsanger" dbkey="phiX" value="hisat_input_1_forward.fastq" />
             <param name="input_2" ftype="fastqsanger" dbkey="phiX" value="hisat_input_1_reverse.fastq" />
-            <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" />
+            <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" sort="true" >
+                <metadata name="sort_order" value="coordinate"/>
+            </output>
         </test>
         <!-- Ensure trimming works -->
         <test expect_num_outputs="1">
@@ -788,7 +797,9 @@
             <param name="trim5" value="15" />
             <param name="input_1" ftype="fastqsanger" value="hisat_input_2_forward.fastq" />
             <param name="input_2" ftype="fastqsanger" value="hisat_input_2_reverse.fastq" />
-            <output name="output_alignments" file="hisat_output_2.bam" ftype="bam" lines_diff="2" />
+            <output name="output_alignments" file="hisat_output_2.bam" ftype="bam" lines_diff="2" sort="true" >
+                <metadata name="sort_order" value="coordinate"/>
+            </output>
         </test>
         <!-- Ensure paired options works -->
         <test expect_num_outputs="1">
@@ -803,7 +814,9 @@
             <param name="paired_options_selector" value="advanced" />
             <param name="no_mixed" value="True" />
             <param name="no_discordant" value="True" />
-            <output name="output_alignments" file="hisat_output_3.bam" ftype="bam" lines_diff="2" />
+            <output name="output_alignments" file="hisat_output_3.bam" ftype="bam" lines_diff="2" sort="true" >
+                <metadata name="sort_order" value="coordinate"/>
+            </output>
         </test>
         <!-- Ensure single unaligned output works -->
         <test expect_num_outputs="2">
@@ -842,7 +855,9 @@
             <param name="paired_options_selector" value="advanced" />
             <param name="no_mixed" value="True" />
             <param name="no_discordant" value="True" />
-            <output name="output_alignments" file="hisat_output_3.bam" ftype="bam" lines_diff="2" />
+            <output name="output_alignments" file="hisat_output_3.bam" ftype="bam" lines_diff="2" sort="true" >
+                <metadata name="sort_order" value="coordinate"/>
+            </output>
         </test>
         <!-- Ensure fastqsanger.bz2 works -->
         <test expect_num_outputs="1">
@@ -857,7 +872,9 @@
             <param name="paired_options_selector" value="advanced" />
             <param name="no_mixed" value="True" />
             <param name="no_discordant" value="True" />
-            <output name="output_alignments" file="hisat_output_3.bam" ftype="bam" lines_diff="2" />
+            <output name="output_alignments" file="hisat_output_3.bam" ftype="bam" lines_diff="2" sort="true" >
+                <metadata name="sort_order" value="coordinate"/>
+            </output>
         </test>
         <!-- Ensure paired strandness works -->
         <test expect_num_outputs="1">
@@ -867,7 +884,9 @@
             <param name="input_1" ftype="fastqsanger" value="hisat_input_1_forward.fastq" />
             <param name="input_2" ftype="fastqsanger" value="hisat_input_1_reverse.fastq" />
             <param name="rna_strandness" value="FR" />
-            <output name="output_alignments" file="hisat_output_4.bam" ftype="bam" lines_diff="2" />
+            <output name="output_alignments" file="hisat_output_4.bam" ftype="bam" lines_diff="2" sort="true" >
+                <metadata name="sort_order" value="coordinate"/>
+            </output>
         </test>
         <!-- Ensure summary file output works -->
         <test expect_num_outputs="2">
@@ -886,7 +905,9 @@
             <param name="source" value="history" />
             <param name="history_item" ftype="fasta" value="phiX.fa" />
             <param name="input_1" ftype="fastqsanger" value="hisat_input_1_interleaved.fastq" />
-            <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" />
+            <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" sort="true" >
+                <metadata name="sort_order" value="coordinate"/>
+            </output>
         </test>
         <!-- Ensure interleaved bz input works -->
         <test expect_num_outputs="1" >
@@ -894,7 +915,9 @@
             <param name="source" value="history" />
             <param name="history_item" ftype="fasta" value="phiX.fa" />
             <param name="input_1" ftype="fastqsanger.bz2" value="hisat_input_1_interleaved.fastq.bz2" />
-            <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" />
+            <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" sort="true" >
+                <metadata name="sort_order" value="coordinate"/>
+            </output>
         </test>
         <!-- Ensure interleaved gz input works -->
         <test expect_num_outputs="1" >
@@ -902,7 +925,9 @@
             <param name="source" value="history" />
             <param name="history_item" ftype="fasta" value="phiX.fa" />
             <param name="input_1" ftype="fastqsanger.gz" value="hisat_input_1_interleaved.fastq.gz" />
-            <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" />
+            <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" sort="true" >
+                <metadata name="sort_order" value="coordinate"/>
+            </output>
         </test>
         <!-- Ensure interleaved fasta input works -->
         <test expect_num_outputs="1" >
@@ -910,7 +935,9 @@
             <param name="source" value="history" />
             <param name="history_item" ftype="fasta" value="phiX.fa" />
             <param name="input_1" ftype="fasta" value="hisat_input_1_interleaved.fasta" />
-            <output name="output_alignments" file="hisat_output_1_noqual.bam" ftype="bam" lines_diff="2" />
+            <output name="output_alignments" file="hisat_output_1_noqual.bam" ftype="bam" lines_diff="2" sort="true" >
+                <metadata name="sort_order" value="coordinate"/>
+            </output>
         </test>
         <!-- Ensure novel splicesite file output works -->
         <test>
@@ -921,7 +948,9 @@
             <param name="rna_strandness" value="R" />
             <param name="adv|spliced_options|spliced_options_selector" value="advanced"/>
             <param name="adv|spliced_options|novel_splicesite_outfile" value="true" />
-            <output name="output_alignments" file="hisat_output_spliced_1.bam" ftype="bam" lines_diff="2" />
+            <output name="output_alignments" file="hisat_output_spliced_1.bam" ftype="bam" lines_diff="2" sort="true" >
+                <metadata name="sort_order" value="coordinate"/>
+            </output>
             <output name="novel_splicesite_output" file="novel_splicesite_out.tab" ftype="tabular" />
         </test>
         <!-- Ensure SAM output settings work -->
@@ -941,7 +970,9 @@
             </repeat>          
             <param name="adv|sam_options|chr_text" value="--add-chrname"/>
             <param name="adv|sam_options|omit_sec_seq" value="True"/>                        
-            <output name="output_alignments" file="hisat_output_5.bam" ftype="bam" lines_diff="2" />
+            <output name="output_alignments" file="hisat_output_5.bam" ftype="bam" lines_diff="2" sort="true" >
+                <metadata name="sort_order" value="coordinate"/>
+            </output>
         </test>
     </tests>