changeset 17:c441583adae5 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"

--- a/fasterq_dump.xml	Fri Mar 20 12:47:18 2020 -0400
+++ b/fasterq_dump.xml	Wed Apr 29 12:12:23 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@VERSION@+galaxy1" profile="18.01">
+<tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@VERSION@+galaxy2" profile="18.01">
     <description>format from NCBI SRA</description>
     <macros>
         <import>sra_macros.xml</import>
@@ -12,41 +12,50 @@
         ln -s '${input.file}' "\$acc" &&
     #end if
     @CONFIGURE_TIMEOUT@
-    fasterq-dump "\$acc" -e \${GALAXY_SLOTS:-1}
-    $adv.split
-    #if str( $adv.minlen ) != "":
-        --min-read-len "$adv.minlen"
-    #end if
-    $adv.skip_technical >> $log 2>&1 
-    &&
+    @CONFIGURE_RETRY@
+    while [ \$SRA_PREFETCH_ATTEMPT -le \$SRA_PREFETCH_RETRIES ] ; do
+        fasterq-dump "\$acc" -e \${GALAXY_SLOTS:-1}
+        $adv.split
+        #if str( $adv.minlen ) != "":
+            --min-read-len "$adv.minlen"
+        #end if
+        $adv.skip_technical >> $log 2>&1 ;
+        if [ \$? == 0 ] ; then
+            break ;
+        else
+            echo "Prefetch attempt \$SRA_PREFETCH_ATTEMPT of \$SRA_PREFETCH_RETRIES exited with code \$?" ;
+            SRA_PREFETCH_ATTEMPT=`expr \$SRA_PREFETCH_ATTEMPT + 1` ;
+            sleep 1 ;
+        fi ;
+    done &&
     mkdir -p output &&
     mkdir -p outputOther &&
     count=`ls *.fastq | wc -l` &&
     echo "There are \$count fastq" &&
     data=(\$(ls *.fastq)) &&
     if [ "\$count" -eq 1 ]; then
-        gzip -c "\${data[0]}" > output/"\${acc}"__single.fastqsanger.gz &&
+        @COMPRESS@ "\${data[0]}" > output/"\${acc}"__single.fastqsanger.gz &&
         rm "\${data[0]}";
     elif [ "$adv.split" = "--split-3" ]; then
         if [ -e "\${acc}".fastq ]; then
-            gzip -c "\${acc}".fastq > outputOther/"\${acc}"__single.fastqsanger.gz;
+            @COMPRESS@ "\${acc}".fastq > outputOther/"\${acc}"__single.fastqsanger.gz;
         fi &&
-        gzip -c "\${acc}"_1.fastq > output/"\${acc}"_forward.fastqsanger.gz &&
-        gzip -c "\${acc}"_2.fastq > output/"\${acc}"_reverse.fastqsanger.gz &&
+        @COMPRESS@ "\${acc}"_1.fastq > output/"\${acc}"_forward.fastqsanger.gz &&
+        @COMPRESS@ "\${acc}"_2.fastq > output/"\${acc}"_reverse.fastqsanger.gz &&
         rm "\${acc}"*.fastq;
     elif [ "\$count" -eq 2 ]; then
         #if $adv.skip_technical:
-            gzip -c "\${data[0]}" > output/"\${acc}"_forward.fastqsanger.gz &&
-            gzip -c "\${data[1]}" > output/"\${acc}"_reverse.fastqsanger.gz &&
+            @COMPRESS@ "\${data[0]}" > output/"\${acc}"_forward.fastqsanger.gz &&
+            @COMPRESS@ "\${data[1]}" > output/"\${acc}"_reverse.fastqsanger.gz &&
         #else
-            gzip -c "\${data[0]}" > outputOther/"\${data[0]}"sanger.gz &&
-            gzip -c "\${data[1]}" > outputOther/"\${data[1]}"sanger.gz &&
+            @COMPRESS@ "\${data[0]}" > outputOther/"\${data[0]}"sanger.gz &&
+            @COMPRESS@ "\${data[1]}" > outputOther/"\${data[1]}"sanger.gz &&
         #end if
         rm "\${data[0]}" &&
         rm "\${data[1]}";
     else
         for file in \${data[*]}; do
-            gzip -c "\$file" > outputOther/"\$file"sanger.gz &&
+            @COMPRESS@ "\$file" > outputOther/"\$file"sanger.gz &&
             rm "\$file";
         done;
     fi;
@@ -81,7 +90,7 @@
              identifier in the nested collection and identifier_1 is either
              forward or reverse (for instance samp1_forward.fq).
         -->
-        
+
             <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.fastqsanger.gz" directory="output" ext="fastqsanger.gz" />
         </collection>
         <collection name="output_collection" type='list' label="Single-end data (fasterq-dump)">
@@ -179,7 +188,7 @@
 
 **Uploading data for a single accession**
 
-When you type a single accession number (e.g., `SRR1582967`) into **Accession** box and click **Execute** the tool will fetch data for you. 
+When you type a single accession number (e.g., `SRR1582967`) into **Accession** box and click **Execute** the tool will fetch data for you.
 
 -----
 
@@ -205,7 +214,7 @@
 
 **Output**
 
-In every case, fastq datasets produced will be saved in Galaxy's history as a collection_ - a single history element containing multiple datasets. 
+In every case, fastq datasets produced will be saved in Galaxy's history as a collection_ - a single history element containing multiple datasets.
 In fact, three collections will be produced: one containing paired-end data, another containing single-end data, and a third one which contains reads which could not be classified.
 Some collections may be empty if the accessions provided in the list does not contain one of the type of data.
 

--- a/sra_macros.xml	Fri Mar 20 12:47:18 2020 -0400
+++ b/sra_macros.xml	Wed Apr 29 12:12:23 2020 -0400
@@ -3,9 +3,14 @@
     <token name="@ACCESSIONS_FROM_FILE@">
         grep '^[[:space:]]*[E|S|D]RR[0-9]\{1,\}[[:space:]]*$'
     </token>
+    <token name="@COMPRESS@"><![CDATA[pigz -cqp \${GALAXY_SLOTS:-1}]]></token>
     <token name="@CONFIGURE_TIMEOUT@"><![CDATA[
         vdb-config --restore-defaults && vdb-config -s /http/timeout/read=10000 || true &&
     ]]></token>
+    <token name="@CONFIGURE_RETRY@"><![CDATA[
+        export SRA_PREFETCH_RETRIES=3 &&
+        export SRA_PREFETCH_ATTEMPT=1 &&
+    ]]></token>
     <token name="@SET_ACCESSIONS@"><![CDATA[
         #if $input.input_select=="file_list":
             for acc in `@ACCESSIONS_FROM_FILE@ '$input.file_list'` ;
@@ -18,6 +23,7 @@
     <macro name="requirements">
         <requirements>
             <requirement type="package" version="2.10.3">sra-tools</requirement>
+            <requirement type="package" version="2.3.4">pigz</requirement>
             <yield/>
         </requirements>
     </macro>