# HG changeset patch
# User iuc
# Date 1584722212 0
# Node ID 54366e4d692a30764fb06ee2e812f1ac2c345b33
# Parent  5c5d6624f8de1568ab911633dee7b47cc3ab50c8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2be63abd7e4db27fa32ecbbc10d48cacb0073115"

diff -r 5c5d6624f8de -r 54366e4d692a fasterq_dump.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fasterq_dump.xml	Fri Mar 20 16:36:52 2020 +0000
@@ -0,0 +1,237 @@
+<tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@VERSION@+galaxy1" profile="18.01">
+    <description>format from NCBI SRA</description>
+    <macros>
+        <import>sra_macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <version_command>fasterq-dump --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+    @SET_ACCESSIONS@
+    #if $input.input_select == "file":
+        acc='${input.file.name}' &&
+        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 >> $log 2>&1 
+    &&
+    mkdir -p output &&
+    mkdir -p outputOther &&
+    count=`ls *.fastq | wc -l` &&
+    echo "There are \$count fastq" &&
+    data=(\$(ls *.fastq)) &&
+    if [ "\$count" -eq 1 ]; then
+        gzip -c "\${data[0]}" > output/"\${acc}"__single.fastqsanger.gz &&
+        rm "\${data[0]}";
+    elif [ "$adv.split" = "--split-3" ]; then
+        if [ -e "\${acc}".fastq ]; then
+            gzip -c "\${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 &&
+        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 &&
+        #else
+            gzip -c "\${data[0]}" > outputOther/"\${data[0]}"sanger.gz &&
+            gzip -c "\${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 &&
+            rm "\$file";
+        done;
+    fi;
+    #if $input.input_select=="file_list":
+        ) ; done
+
+        ;
+    #elif  $input.input_select=="accession_number":
+    );
+    #end if
+    ]]>
+    </command>
+    <inputs>
+        <expand macro="input_conditional"/>
+        <section name="adv" title="Advanced Options" expanded="False">
+            <param name="minlen" type="integer" label="Minimum read length" optional="true" help="Filter by sequence length. Will dump only reads longer or equal to this value." argument="--min-read-len"/>
+            <param name="split" type="select" display="radio" label="Select how to split the spots" help="This option will only be used when there are multiple reads per spot (for example paired-end).">
+                <option value="--split-3">--split-3: write properly paired biological reads into different files and single reads in another file</option>
+                <option value="--split-files">--split-files: write reads into different files (forward and reverse may not match if one read is empty)</option>
+                <option value="--split-spot">--split-spot: split spots into reads (only one output file)</option>
+                <option value="--concatenate-reads">--concatenate-reads: writes whole spots into one file</option>
+            </param>
+            <param name="skip_technical" type="boolean" truevalue="--skip-technical" falsevalue="--include-technical" checked="True" label="Dump only biological reads" help="Will not be used if --split-3 is selected." argument="--skip-technical/--include-technical"/>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="log" format="txt" label="fasterq-dump log"/>
+        <collection name="list_paired" type="list:paired" label="Pair-end data (fasterq-dump)">
+
+        <!-- Use named regex group to grab pattern
+             <identifier_0>_<identifier_1>.fq. Here identifier_0 is the list
+             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)">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)__single\.fastqsanger.gz" directory="output" ext='fastqsanger.gz'/>
+        </collection>
+        <collection name="output_collection_other" type='list' label="Other data (fasterq-dump)">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fastqsanger\.gz" directory="outputOther" format="fastqsanger.gz"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_select" value="accession_number"/>
+            <param name="accession" value="ERR086330"/>
+            <output_collection name="list_paired" type="list:paired">
+                <element name="ERR086330">
+                    <element name="forward" file="ERR086330_1.fastq.gz" decompress="True">
+                    </element>
+                    <element name="reverse" file="ERR086330_2.fastq.gz" decompress="True">
+                    </element>
+                </element>
+            </output_collection>
+        </test>
+        <test>
+            <param name="input_select" value="accession_number"/>
+            <param name="accession" value="SRR002702"/>
+            <param name="split" value="--split-files"/>
+            <param name="skip_technical" value="False"/>
+            <output_collection name="output_collection_other" type="list">
+                <element name="SRR002702_1" file="SRR002702_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
+                <element name="SRR002702_2" file="SRR002702_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
+            </output_collection>
+        </test>
+        <test>
+            <param name="input_select" value="file"/>
+            <param name="file" value="SRR522874.sra"/>
+            <param name="split" value="--split-files"/>
+            <param name="skip_technical" value="True"/>
+            <output_collection name="list_paired" type="list:paired">
+                <element name="SRR522874.sra">
+                    <element name="forward" file="SRR522874.sra_2.fastq.gz" decompress="True">
+                    </element>
+                    <element name="reverse" file="SRR522874.sra_4.fastq.gz" decompress="True">
+                    </element>
+                </element>
+            </output_collection>
+        </test>
+        <test>
+            <param name="input_select" value="file"/>
+            <param name="file" value="SRR522874.sra"/>
+            <param name="split" value="--split-files"/>
+            <param name="skip_technical" value="False"/>
+            <output_collection name="output_collection_other" type="list">
+                <element name="SRR522874.sra_1" file="SRR522874.sra_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
+                <element name="SRR522874.sra_2" file="SRR522874.sra_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
+                <element name="SRR522874.sra_3" file="SRR522874.sra_3.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
+                <element name="SRR522874.sra_4" file="SRR522874.sra_4.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
+            </output_collection>
+        </test>
+        <test>
+            <param name="input_select" value="file_list"/>
+            <param name="file_list" value="list_sra"/>
+            <param name="minlen" value="21"/>
+            <output_collection name="output_collection_other" type="list">
+                <element name="SRR522874__single" file="SRR522874.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
+            </output_collection>
+            <output_collection name="list_paired" type="list:paired">
+                <element name="SRR522874">
+                    <element name="forward" file="SRR522874_1.fastq.gz" decompress="True">
+                    </element>
+                    <element name="reverse" file="SRR522874_2.fastq.gz" decompress="True">
+                    </element>
+                </element>
+            </output_collection>
+            <output_collection name="output_collection" type="list">
+                <element name="SRR002702" file="SRR002702_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does?**
+
+This tool extracts data (in fastq_ format) from the Short Read Archive (SRA) at the National Center for Biotechnology Information (NCBI). It is based on the fasterq-dump_ utility of the SRA Toolkit.
+
+**How to use it?**
+
+There are three ways in which you can download data:
+
+ 1. Data for single accession
+ 2. Multiple datasets using a list of accessions
+ 3. Extract data from already uploaded SRA dataset
+
+Below we discuss each in detail.
+
+------
+
+**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. 
+
+-----
+
+**Uploading multiple datasets using a list of accessions**
+
+A more realistic scenario is when you want to upload a number of datasets at once. To do this you need a list of accession, where there is only one accession per line (see below for information on how to generate such a file). Once you have this file:
+
+ 1. Upload it into your history using Galaxy's upload tool
+ 2. Once the list of accessions is uploaded choose *List of SRA accessions, one per line* from **select input type** dropdown
+ 3. Choose uploaded file within the **sra accession list** field
+ 4. Click **Execute**
+
+-----
+
+**Extract data from already uploaded SRA dataset**
+
+If a SRA dataset is present in the history, it can be converted into fastq dataset by setting **select input type** drop-down to *SRA archive in current history*. Just like in the case of extracting data for single accession number the following applies:
+
+ - if data is paired-ended (or mate-pair) the tool will generate a single *interleaved* dataset, in which forward and reverse mates are alternating (see example below).
+ - if data is single ended, a standard fastq dataset will be produced
+
+-----
+
+**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 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.
+
+.. class:: warningmark
+
+When you decide to dump technical reads (in Advanced Options Dump only biological reads is set to No), you will probably find your PAIRED data in the other data collection as it is impossible to determine if it was 2 biological reads or one biological and one technical.
+
+.. class:: warningmark
+
+By default, only biological reads are dumped and in case of PAIRED dataset only the spots which have both reads will be in the paired-end collection. The remaining single reads will be in the other colletion.
+To keep all reads, and maybe do not have the same number of reads in forward and reverse use the --split-files option in Advanced Options, Select how to split the spots.
+
+@ACCESSION_LIST_HOWTO@
+
+-----
+
+
+.. _fastq: https://en.wikipedia.org/wiki/FASTQ_format
+.. _fastq-dump: https://ncbi.github.io/sra-tools/fastq-dump.html
+.. _fasterq-dump: https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump
+.. _collection: https://galaxyproject.org/tutorials/collections/
+.. _link: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies
+
+@SRATOOLS_ATTRRIBUTION@
+
+]]>
+    </help>
+    <expand macro="citation"/>
+  </tool>
diff -r 5c5d6624f8de -r 54366e4d692a fastq_dump.xml
--- a/fastq_dump.xml	Tue Dec 04 15:00:32 2018 -0500
+++ b/fastq_dump.xml	Fri Mar 20 16:36:52 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" version="@VERSION@.3">
+<tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" version="@VERSION@+galaxy1" profile="18.01">
     <description>format from NCBI SRA</description>
     <macros>
         <import>sra_macros.xml</import>
@@ -6,14 +6,12 @@
     <expand macro="requirements"/>
     <version_command>fastq-dump --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
-
     @SET_ACCESSIONS@
 
     ## Need to set the home directory to the current working directory,
     ## else the tool tries to write to home/.ncbi and fails when used
     ## with a cluster manager.
-    export HOME=\$PWD &&
-    vdb-config --restore-defaults &&
+    @CONFIGURE_TIMEOUT@
     #if $input.input_select == "file":
         fastq-dump --log-level fatal --accession '${input.file.name}'
     #else:
@@ -21,9 +19,7 @@
         ## Do not use prefetch if region is specified, to avoid downloading
         ## the complete sra file.
         #if ( str( $adv.region ) == "" ) and ( str( $adv.minID ) == "" ) and ( str( $adv.maxID ) == "" ):
-            ASCP_PATH=`command -v ascp` &&
-            ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true &&
-            prefetch -X 200G --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "\$acc" &&
+            prefetch -X 200000000 "\$acc" &&
             ## Duplicate vdb-config, in case settings changed between prefetch and
             ## dump command.
             vdb-config -s "/repository/user/main/public/root=\$PWD" &&
@@ -70,6 +66,12 @@
     #elif str( $outputformat ) == "fastqsanger.bz2":   
         --bzip2
     #end if
+
+    #if str($adv.table) != "":
+        --table $adv.table
+    #end if
+
+
     #if $input.input_select=="file":
         --stdout
         "$input.file" > "$output_file"
@@ -80,6 +82,7 @@
     #end if
 
     #if $input.input_select=="file_list":
+        "\$acc"
         ) ; done
 
         ;
@@ -126,6 +129,7 @@
             <param name="spotgroups" type="text" label="Filter by spot-groups" optional="true" argument="--spot-groups"/>
             <param name="clip" type="boolean" truevalue="--clip" falsevalue="" argument="--clip" label="Apply left and right clips" />
             <param name="skip_technical" type="boolean" truevalue="--skip-technical" falsevalue="" checked="False" label="Dump only biological reads" argument="--skip-technical"/>
+            <param name="table" label="Table name within cSRA object" type="text" value="" optional="true" help="For SRA of noisy long-reads put SEQUENCE" argument="--table"/>
         </section>
     </inputs>
     <outputs>
@@ -226,7 +230,15 @@
             <output_collection name="output_collection" type="list">
                 <element name="SRR1993644" file="SRR1993644.fastqsanger"/>
             </output_collection>
-        </test>            
+        </test>
+        <test>
+            <param name="input_select" value="accession_number"/>
+            <param name="outputformat" value="fastqsanger.gz"/>
+            <param name="accession" value="SRR6982805"/>
+            <param name="maxID" value="2"/>
+            <param name="table" value="SEQUENCE"/>
+            <output name="output_accession" file="SRR6982805.fastqsanger.gz" ftype="fastqsanger.gz" decompress="True"/>
+        </test>  
     </tests>
     <help><![CDATA[
 **What it does?**
diff -r 5c5d6624f8de -r 54366e4d692a sam_dump.xml
--- a/sam_dump.xml	Tue Dec 04 15:00:32 2018 -0500
+++ b/sam_dump.xml	Fri Mar 20 16:36:52 2020 +0000
@@ -1,9 +1,11 @@
-<tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@.4">
+<tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@+galaxy1" profile="18.01">
     <description>format from NCBI SRA</description>
     <macros>
         <import>sra_macros.xml</import>
     </macros>
-    <expand macro="requirements"/>
+    <expand macro="requirements">
+        <requirement type="package" version="1.10">samtools</requirement>
+    </expand>
     <version_command>sam-dump --version</version_command>
     <command detect_errors="exit_code">
 <![CDATA[
@@ -12,8 +14,7 @@
         ## Need to set the home directory to the current working directory,
         ## else the tool tries to write to home/.ncbi and fails when used
         ## with a cluster manager.
-        export HOME=\$PWD &&
-        vdb-config --restore-defaults &&
+        @CONFIGURE_TIMEOUT@
         vdb-config -s "/repository/user/main/public/root=\$PWD" &&
         ## Do not use prefetch if region is specified, to avoid downloading
         ## the complete sra file.
@@ -22,9 +23,7 @@
             sam-dump --log-level fatal  '${input.file.name}'
         #else:
             #if ( str( $adv.region ) == "" ):
-                ASCP_PATH=`command -v ascp` &&
-                ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true &&
-                prefetch -X 200G --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "\$acc" &&
+                prefetch -X 200000000 "\$acc" &&
                 ## Duplicate vdb-config, in case settings changed between prefetch and
                 ## dump command.
                 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
diff -r 5c5d6624f8de -r 54366e4d692a sra_macros.xml
--- a/sra_macros.xml	Tue Dec 04 15:00:32 2018 -0500
+++ b/sra_macros.xml	Fri Mar 20 16:36:52 2020 +0000
@@ -1,8 +1,11 @@
 <macros>
-    <token name="@VERSION@">2.9.1</token>
+    <token name="@VERSION@">2.10.4</token>
     <token name="@ACCESSIONS_FROM_FILE@">
         grep '^[[:space:]]*[E|S|D]RR[0-9]\{1,\}[[:space:]]*$'
     </token>
+    <token name="@CONFIGURE_TIMEOUT@"><![CDATA[
+        vdb-config --restore-defaults && vdb-config -s /http/timeout/read=10000 || true &&
+    ]]></token>
     <token name="@SET_ACCESSIONS@"><![CDATA[
         #if $input.input_select=="file_list":
             for acc in `@ACCESSIONS_FROM_FILE@ '$input.file_list'` ;
@@ -14,8 +17,8 @@
 
     <macro name="requirements">
         <requirements>
-            <requirement type="package" version="2.9.1">sra-tools</requirement>
-            <requirement type="package" version="1.9">samtools</requirement>
+            <requirement type="package" version="2.10.3">sra-tools</requirement>
+            <yield/>
         </requirements>
     </macro>
     <macro name="sanitize_query">
diff -r 5c5d6624f8de -r 54366e4d692a sra_pileup.xml
--- a/sra_pileup.xml	Tue Dec 04 15:00:32 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,99 +0,0 @@
-<tool id="sra_pileup" name="Download and Generate Pileup Format" version="@VERSION@.2">
-    <description>from NCBI SRA</description>
-    <macros>
-        <import>sra_macros.xml</import>
-    </macros>
-    <expand macro="requirements"/>
-    <version_command>sra-pileup --version</version_command>
-    <command detect_errors="exit_code">
-        <![CDATA[
-
-        #if $input.input_select=="accession_number":
-            acc='${input.accession}' && [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] &&
-        #end if
-
-        ## Need to set the home directory to the current working directory,
-        ## else the tool tries to write to home/.ncbi and fails when used
-        ## with a cluster manager.
-        export HOME=\$PWD &&
-        vdb-config --restore-defaults &&
-        vdb-config -s "/repository/user/main/public/root=\$PWD" &&
-        #if ( str( $adv.region ) == "" ):
-            ASCP_PATH=`command -v ascp` &&
-            ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true &&
-            prefetch -X 200G --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "\$acc" &&
-            ## Duplicate vdb-config, in case settings changed between prefetch and
-            ## sra-pileup command.
-            vdb-config -s "/repository/user/main/public/root=\$PWD" &&
-        #end if
-        sra-pileup --log-level fatal
-        #if str( $adv.region ) != "":
-            --aligned-region "$adv.region"
-        #end if
-        #if str( $adv.minMapq ) != "":
-            --minmapq "$adv.minMapq"
-        #end if
-        #if $input.input_select == "file":
-            "$input.file" > "$output_file"
-        #elif $input.input_select == "accession_number":
-            "\$acc" > "$output_accession"
-        #elif $input.input_select == "text":
-            `@ACCESSIONS_FROM_FILE@ '$input.text'` > "$output_text"
-        #end if
-        ]]>
-    </command>
-    <inputs>
-        <conditional name="input">
-            <param name="input_select" type="select" label="select input type">
-                <option value="accession_number">SRR accession</option>
-                <option value="file">SRA archive in current history</option>
-                <option value="text">text file containing SRR accession</option>
-            </param>
-            <when value="file">
-                <param format="sra" name="file" type="data" label="sra archive"/>
-            </when>
-            <when value="accession_number">
-                <param format="text" name="accession" type="text" label="SRR accession" help="Must start with SRR, e.g. SRR925743">
-                    <expand macro="sanitize_query" />
-                </param>
-            </when>
-            <when value="text">
-                <param format="txt" name="text" type="data" label="text file"/>
-            </when>
-        </conditional>
-        <section name="adv" title="Advanced Options" expanded="False">
-            <expand macro="region"/>
-          <expand macro="minMapq"/>
-        </section>
-    </inputs>
-    <outputs>
-        <data format="pileup" name="output_accession" label="${input.accession} (sra-pileup)">
-            <filter>input['input_select'] == "accession_number"</filter>
-        </data>
-        <data format="pileup" name="output_file" label="${input.file.name} (sra-pileup)">
-            <filter>input['input_select'] == "file"</filter>
-        </data>
-        <data format="pileup" name="output_text" label="${input.text.name} (sra-pileup)">
-            <filter>input['input_select'] == "text"</filter>
-        </data>
-    </outputs>
-    <tests>
-        <test>
-            <param name="input_select" value="accession_number"/>
-            <param name="accession" value="SRR925743"/>
-            <param name="region" value="17:41243452-41277500"/>
-            <output name="output_accession" file="sra_pileup_result.pileup" compare="contains" ftype="pileup"/>
-        </test>
-    </tests>
-    <help>
- <![CDATA[
-
-This tool produces pileup format from sra archives using sra-pileup.
-The sra-pileup program is developed at NCBI, and is available at
-http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
-@SRATOOLS_ATTRRIBUTION@
-
-]]>
-    </help>
-    <expand macro="citation"/>
-</tool>
diff -r 5c5d6624f8de -r 54366e4d692a test-data/ERR086330_1.fastq.gz
Binary file test-data/ERR086330_1.fastq.gz has changed
diff -r 5c5d6624f8de -r 54366e4d692a test-data/ERR086330_2.fastq.gz
Binary file test-data/ERR086330_2.fastq.gz has changed
diff -r 5c5d6624f8de -r 54366e4d692a test-data/SRR002702_1.fastq.gz
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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@@ -0,0 +1,2 @@
+SRR522874
+SRR002702