diff umi-tools_counts.xml @ 12:71ad4a56c40c draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bc1b362f6783d3fc0ed0f42c14687001d7ff5f7a

--- a/umi-tools_counts.xml	Sat Sep 28 16:40:55 2024 +0000
+++ b/umi-tools_counts.xml	Sat Oct 05 13:08:27 2024 +0000
@@ -1,9 +1,9 @@
 <tool id="umi_tools_count" name="UMI-tools count" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>performs quantification of UMIs from BAM files</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements">
         <!-- TODO see comment in LINK_SAM_BAM_INPUT -->
         <requirement type="package" version="1.12">samtools</requirement>
@@ -33,7 +33,7 @@
     ]]></command>
     <inputs>
         <param name="input" type="data" format="sam,bam" label="Reads to deduplicate in SAM or BAM format" help="Please use the samtools sort tool to ensure a correct BAM input" />
-        <param argument="--wide-format-cell-counts" name="wide_format_cell_counts" type="boolean" truevalue="--wide-format-cell-counts" falsevalue="" checked="true" label="Output a matrix of genes and cells, instead of a flat file" />
+        <param name="wide_format_cell_counts" type="boolean" truevalue="--wide-format-cell-counts" falsevalue="" checked="true" label="Output a matrix of genes and cells, instead of a flat file" />
         <expand macro="barcode_options_macro"/>
         <expand macro="umi_grouping_options_macro"/>
         <expand macro="sambam_options_macro"/>
@@ -66,7 +66,7 @@
         <expand macro="log_output_macro"/>
     </outputs>
     <tests>
-        <test><!--count_single_gene_tag:-->
+        <test expect_num_outputs="1"><!--count_single_gene_tag:-->
             <param name="input" value="chr19_gene_tags.bam" />
             <section name="advanced">
                 <param name="random_seed" value="123456789" />
@@ -85,7 +85,7 @@
             <param name="wide_format_cell_counts" value="false" />
             <output name="out_counts" value="count_single_gene_tag.tsv" />
         </test>
-        <test><!--count_single_gene_tag .. with sam input-->
+        <test expect_num_outputs="1"><!--count_single_gene_tag .. with sam input-->
             <param name="input" value="chr19_gene_tags.sam" />
             <section name="advanced">
                 <param name="random_seed" value="123456789" />
@@ -104,7 +104,7 @@
             <param name="wide_format_cell_counts" value="false" />
             <output name="out_counts" value="count_single_gene_tag.tsv" />
         </test>
-        <test><!--count_single_cells_gene_tag:-->
+        <test expect_num_outputs="1"><!--count_single_cells_gene_tag:-->
             <param name="input" value="chr19_gene_tags.bam" />
             <section name="advanced">
                 <param name="random_seed" value="123456789" />
@@ -123,7 +123,7 @@
             <param name="wide_format_cell_counts" value="false" />
             <output name="out_counts" value="count_single_cells_gene_tag.tsv" />
         </test>
-        <test><!--count_single_cells_wide_gene_tag:-->
+        <test expect_num_outputs="1"><!--count_single_cells_wide_gene_tag:-->
             <param name="input" value="chr19_gene_tags.bam" />
             <section name="advanced">
                 <param name="random_seed" value="123456789" />
@@ -142,7 +142,7 @@
             <param name="wide_format_cell_counts" value="true" />
             <output name="out_counts" value="count_single_cells_gene_tag_wide.tsv" />
         </test>
-        <test><!-- count ENSDARG00000019692, with defaults -->
+        <test expect_num_outputs="1"><!-- count ENSDARG00000019692, with defaults -->
             <param name="input" value="fc.ENSDARG00000019692.bam" />
             <section name="advanced">
                 <param name="random_seed" value="0" />
@@ -156,7 +156,7 @@
             </section>
             <output name="out_counts" value="fc.ENSDARG00000019692.counts" />
         </test>
-        <test><!-- count ENSDARG00000019692, relabel string -->
+        <test expect_num_outputs="1"><!-- count ENSDARG00000019692, relabel string -->
             <param name="input" value="fc.ENSDARG00000019692.bam" />
             <section name="advanced">
                 <param name="random_seed" value="0" />
@@ -174,7 +174,7 @@
             </conditional>
             <output name="out_counts" value="fc.ENSDARG00000019692.counts.test" />
         </test>
-        <test><!-- count ENSDARG00000019692, relabel filename -->
+        <test expect_num_outputs="1"><!-- count ENSDARG00000019692, relabel filename -->
             <param name="input" value="fc.ENSDARG00000019692.bam" />
             <section name="advanced">
                 <param name="random_seed" value="0" />