diff alevin.xml @ 10:e4c01dcece8b draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"

--- a/alevin.xml	Wed Mar 24 20:15:12 2021 +0000
+++ b/alevin.xml	Thu Jul 22 14:05:58 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="alevin" name="Alevin" version="@VERSION@+galaxy2">
+<tool id="alevin" name="Alevin" version="@VERSION@+@GALAXY_VERSION@" profile="@PROFILE_VERSION@">
     <description>Quantification and analysis of 3’ tagged-end single-cell sequencing data</description>
     <macros>
         <import>macros.xml</import>
@@ -46,12 +46,16 @@
         && ln -s '${tgmap}' ./alevinmap.tsv
         && salmon alevin -l
         #if $pairstraight.readselect == 'paired':
-            ${pairstraight.orientation}${pairstraight.strandedness}
+            #if $pairstraight.libtype.strandedness == 'A'
+                A
+            #else
+                ${pairstraight.libtype.orientation}${pairstraight.libtype.strandedness}
+            #end if
             -i $index_path
             -1 ./mate1.fastq
             -2 ./mate2.fastq
         #else:
-            '${pairstraight.strandedness}'
+            '${pairstraight.libtype.strandedness}'
             -i $index_path
             -r zcat ./unmate.fastq
         #end if
@@ -126,12 +130,11 @@
             <when value="paired">
                 <param name="file1" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" help="CB+UMI raw sequence file(s)"/>
                 <param name="file2" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" help="Read-sequence file(s)"/>
-                <expand macro="orient"/>
-                <expand macro="stranded"/>
+                <expand macro="stranded_pe"/>
             </when>
             <when value="unmated">
                 <param name="unmatedreads" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" label="Unmated reads files"/>
-                <expand macro="stranded"/>
+                <expand macro="stranded_se"/>
             </when>
         </conditional>
         <param name="protocol" type="select">
@@ -165,24 +168,24 @@
         </section>
     </inputs>
     <outputs>
-        <data name="quants_mat.tsv" label="quants_mat.tsv" format="txt" from_work_dir="quants_mat.tsv">
+        <data name="quants_mat_tsv" label="quants_mat.tsv" format="txt" from_work_dir="quants_mat.tsv">
             <filter>optional["dumpMtx"] is not True</filter>
         </data>
-        <data name="quants_mat.mtx" label="quants_mat.mtx" format="mtx" from_work_dir="output/alevin/quants_mat.mtx">
+        <data name="quants_mat_mtx" label="quants_mat.mtx" format="mtx" from_work_dir="output/alevin/quants_mat.mtx">
             <filter>optional["dumpMtx"]</filter>
         </data>
-        <data name="raw_cb_frequency.txt" label="raw_cb_frequency.txt" format="txt" from_work_dir="output/alevin/raw_cb_frequency.txt">
+        <data name="raw_cb_frequency_txt" label="raw_cb_frequency.txt" format="txt" from_work_dir="output/alevin/raw_cb_frequency.txt">
             <filter>optional["dumpFeatures"]</filter>
         </data>
-        <data name="quants_mat_cols.txt" label="quants_mat_cols.txt" format="txt" from_work_dir="output/alevin/quants_mat_cols.txt"/>
-        <data name="quants_mat_rows.txt" label="quants_mat_rows.txt" format="txt" from_work_dir="output/alevin/quants_mat_rows.txt"/>
+        <data name="quants_mat_cols_txt" label="quants_mat_cols.txt" format="txt" from_work_dir="output/alevin/quants_mat_cols.txt"/>
+        <data name="quants_mat_rows_txt" label="quants_mat_rows.txt" format="txt" from_work_dir="output/alevin/quants_mat_rows.txt"/>
         <data name="quants_tier_mat" label="quants_tier_mat" format="mtx" from_work_dir="output/alevin/quants_tier_mat"/>
-        <data name="alevin.log" label="alevin.log" format="txt" from_work_dir="output/alevin/alevin.log">
+        <data name="alevin_log" label="alevin.log" format="txt" from_work_dir="output/alevin/alevin.log">
             <filter>allout</filter>
         </data>
-        <data name="featureDump.txt" label="featureDump.txt" format="txt" from_work_dir="output/alevin/featureDump.txt"/>
-        <data name="whitelist.txt" label="whitelist.txt" format="txt" from_work_dir="output/alevin/whitelist.txt"/>
-        <data name="bfh.txt" label="bfh.txt" format="txt" from_work_dir="output/alevin/bfh.txt">
+        <data name="featureDump_txt" label="featureDump.txt" format="txt" from_work_dir="output/alevin/featureDump.txt"/>
+        <data name="whitelist_txt" label="whitelist.txt" format="txt" from_work_dir="output/alevin/whitelist.txt"/>
+        <data name="bfh_txt" label="bfh.txt" format="txt" from_work_dir="output/alevin/bfh.txt">
             <filter>optional["dumpBfh"]</filter>
         </data>
         <data name="quants_mean_mat" label="quants_mean_mat" format="mtx" from_work_dir="output/alevin/quants_mean_mat">
@@ -191,23 +194,23 @@
         <data name="quants_var_mat" label="quants_var_mat" format="mtx" from_work_dir="output/alevin/quants_var_mat">
             <filter>optional["numCellBootstraps"]</filter>
         </data>
-        <data name="quants_boot_rows.txt" label="quants_boot_rows.txt" format="txt" from_work_dir="output/alevin/quants_boot_rows.txt">
+        <data name="quants_boot_rows_txt" label="quants_boot_rows.txt" format="txt" from_work_dir="output/alevin/quants_boot_rows.txt">
             <filter>optional["numCellBootstraps"]</filter>
         </data>
-        <data name="alevinmeta_info.json" format="json" label="meta_info.json" from_work_dir="output/aux_info/alevin_meta_info.json">
+        <data name="alevinmeta_info_json" format="json" label="meta_info.json" from_work_dir="output/aux_info/alevin_meta_info.json">
             <filter>allout</filter>
         </data>
-        <data name="ambig_info.tsv" format="tsv" label="ambig_info.tsv" from_work_dir="output/aux_info/ambig_info.tsv">
+        <data name="ambig_info_tsv" format="tsv" label="ambig_info.tsv" from_work_dir="output/aux_info/ambig_info.tsv">
             <filter>allout</filter>
         </data>
-        <data name="meta_info.json" format="json" label="meta_info.json" from_work_dir="output/aux_info/meta_info.json">
+        <data name="meta_info_json" format="json" label="meta_info.json" from_work_dir="output/aux_info/meta_info.json">
             <filter>allout</filter>
         </data>
         <data name="expected_bias" format="txt" label="expected_bias" from_work_dir="output/aux_info/fld"/>
         <data name="observed_bias" format="txt" label="observed_bias" from_work_dir="output/aux_info/observed_bias"/>
         <data name="observed_bias_3p" format="txt" label="observed_bias_3p" from_work_dir="output/aux_info/observed_bias_3p"/>
-        <data name="flenDist.txt" format="txt" label="flenDist.txt" from_work_dir="output/libParams/flenDist.txt"/>
-        <data name="salmon_quant.log" format="txt" label="salmon_quant.log" from_work_dir="output/logs/salmon_quant.log">
+        <data name="flenDist_txt" format="txt" label="flenDist.txt" from_work_dir="output/libParams/flenDist.txt"/>
+        <data name="salmon_quant_log" format="txt" label="salmon_quant.log" from_work_dir="output/logs/salmon_quant.log">
             <filter>allout</filter>
         </data>
         <collection name="umigraphs" type="list" label="Umi graph PDFs">
@@ -241,7 +244,7 @@
                 <param name="freqThreshold" value="5"/>
                 <param name="dumpMtx" value="Yes"/>
             </section>
-            <output name="quants_mat.mtx" file="alevin_mat.mtx" ftype="mtx"/>
+            <output name="quants_mat_mtx" file="alevin_mat.mtx" ftype="mtx" sort="true" lines_diff="62"/>
         </test>
         <test expect_num_outputs="14">
             <conditional name="refTranscriptSource">
@@ -266,7 +269,7 @@
                 <param name="freqThreshold" value="5"/>
                 <param name="dumpMtx" value="Yes"/>
             </section>
-            <output name="quants_mat.mtx" file="alevin_mat.mtx" ftype="mtx"/>
+            <output name="quants_mat_mtx" file="alevin_mat.mtx" ftype="mtx" sort="true" lines_diff="62"/>
         </test>
     </tests>
     <help><![CDATA[