Mercurial > repos > iuc > sra_tools

changeset 26:83c7d564b128 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 21f935ba50d3e4b455246c681e54d5c57c67032f"
author iuc
date Fri, 03 Sep 2021 16:17:53 +0000
parents 69ebb7f46e45
children 9a776b080193
files fasterq_dump.xml fastq_dump.xml sam_dump.xml sra_macros.xml
diffstat 4 files changed, 13 insertions(+), 22 deletions(-) [+]
line wrap: on
line diff
--- a/fasterq_dump.xml	Tue Apr 27 08:55:34 2021 +0000
+++ b/fasterq_dump.xml	Fri Sep 03 16:17:53 2021 +0000
@@ -1,5 +1,6 @@
-<tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@VERSION@+galaxy0" profile="18.01">
+<tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@VERSION@+galaxy1" profile="18.01">
     <description>format from NCBI SRA</description>
+    <expand macro="bio_tools"/>
     <macros>
         <import>sra_macros.xml</import>
     </macros>
@@ -14,11 +15,8 @@
         ln -s '${input.file}' "\$acc" &&
     #end if
     @CONFIGURE_RETRY@
-    ## fetch from public s3 bucket if we can
-    export acc_or_path="\$acc" &&
-    aws s3 cp --no-sign-request "s3://sra-pub-sars-cov2/run/\$acc/\$acc" "\$acc.sra" 2>&1 | tee '$log' && export acc_or_path="\$acc.sra"|| true &&
     while [ \$SRA_PREFETCH_ATTEMPT -le \$SRA_PREFETCH_RETRIES ] ; do
-        fasterq-dump "\$acc_or_path" -e \${GALAXY_SLOTS:-1}
+        fasterq-dump "\$acc" -e \${GALAXY_SLOTS:-1}
         $adv.split
         #if str( $adv.minlen ) != "":
             --min-read-len "$adv.minlen"
@@ -181,19 +179,6 @@
                 </element>
             </output_collection>
         </test>
-        <test expect_num_outputs="4">
-             <!-- test accession downloaded from public bucket -->
-            <param name="input_select" value="accession_number"/>
-            <param name="accession" value="SRR11859153"/>
-            <output_collection name="output_collection" type="list" count="1">
-                <element name="SRR11859153" file="SRR11859153.fastq.gz" decompress="True"/>
-            </output_collection>
-            <output name="log">
-                <assert_contents>
-                    <has_text text="download: s3://sra-pub-sars-cov2/"/>
-                </assert_contents>
-            </output>
-        </test>
     </tests>
     <help><![CDATA[
 **What it does?**
@@ -259,7 +244,7 @@
 
 
 .. _fastq: https://en.wikipedia.org/wiki/FASTQ_format
-.. _fastq-dump: https://ncbi.github.io/sra-tools/fastq-dump.html
+.. _fastq-dump: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=fastq-dump
 .. _fasterq-dump: https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump
 .. _collection: https://galaxyproject.org/tutorials/collections/
 .. _link: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies
--- a/fastq_dump.xml	Tue Apr 27 08:55:34 2021 +0000
+++ b/fastq_dump.xml	Fri Sep 03 16:17:53 2021 +0000
@@ -1,5 +1,6 @@
 <tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" version="@VERSION@+galaxy0" profile="18.01">
     <description>format from NCBI SRA</description>
+    <expand macro="bio_tools"/>
     <macros>
         <import>sra_macros.xml</import>
     </macros>
@@ -335,7 +336,7 @@
 
 
 .. _fastq: https://en.wikipedia.org/wiki/FASTQ_format
-.. _fastq-dump: https://ncbi.github.io/sra-tools/fastq-dump.html
+.. _fastq-dump: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=fastq-dump
 .. _collection: https://galaxyproject.org/tutorials/collections/
 .. _link: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies
 
--- a/sam_dump.xml	Tue Apr 27 08:55:34 2021 +0000
+++ b/sam_dump.xml	Fri Sep 03 16:17:53 2021 +0000
@@ -1,5 +1,6 @@
 <tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@+galaxy0" profile="18.01">
     <description>format from NCBI SRA</description>
+    <expand macro="bio_tools"/>
     <macros>
         <import>sra_macros.xml</import>
     </macros>
@@ -167,7 +168,7 @@
 -----
 
 .. _BAM: https://samtools.github.io/hts-specs/SAMv1.pdf
-.. _sam-dump: https://ncbi.github.io/sra-tools/sam-dump.html
+.. _sam-dump: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=sam-dump
 .. _collection: https://galaxyproject.org/tutorials/collections/
 .. _link: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies
 
--- a/sra_macros.xml	Tue Apr 27 08:55:34 2021 +0000
+++ b/sra_macros.xml	Fri Sep 03 16:17:53 2021 +0000
@@ -8,6 +8,11 @@
         export SRA_PREFETCH_RETRIES=3 &&
         export SRA_PREFETCH_ATTEMPT=1 &&
     ]]></token>
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">sra-tools</xref>
+        </xrefs>
+    </xml>
     <token name="@COPY_CONFIGFILE@"><![CDATA[
     mkdir -p ~/.ncbi &&
     cp '$user_settings_mkfg' ~/.ncbi/user-settings.mkfg &&
@@ -35,7 +40,6 @@
     <macro name="requirements">
         <requirements>
             <requirement type="package" version="@VERSION@">sra-tools</requirement>
-            <requirement type="package" version="1.18.222">awscli</requirement>
             <requirement type="package" version="2.5">pigz</requirement>
             <yield/>
         </requirements>