| Previous changeset 13:c38286ea7047 (2018-10-17) Next changeset 15:f5ea3ce9b9b0 (2019-09-10) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 30ec06de1f3056967f5cc2d8ef57f9692d5533d7 |
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modified:
sam_dump.xml sra_macros.xml |
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| diff -r c38286ea7047 -r 1790dcf3c32d sam_dump.xml --- a/sam_dump.xml Wed Oct 17 11:44:12 2018 -0400 +++ b/sam_dump.xml Tue Dec 04 15:00:55 2018 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@.3"> +<tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@.4"> <description>format from NCBI SRA</description> <macros> <import>sra_macros.xml</import> @@ -17,15 +17,21 @@ vdb-config -s "/repository/user/main/public/root=\$PWD" && ## Do not use prefetch if region is specified, to avoid downloading ## the complete sra file. - #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 - ## dump command. - vdb-config -s "/repository/user/main/public/root=\$PWD" && + + #if $input.input_select == "file": + sam-dump --log-level fatal '${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" && + ## Duplicate vdb-config, in case settings changed between prefetch and + ## dump command. + vdb-config -s "/repository/user/main/public/root=\$PWD" && + #end if + sam-dump --log-level fatal --disable-multithreading #end if - sam-dump --log-level fatal --disable-multithreading + #if str( $adv.region ) != "": --aligned-region '$adv.region' #end if @@ -39,6 +45,7 @@ #if str( $adv.alignments ) == "both": --unaligned #end if + #if str( $adv.alignments ) == "unaligned": --unaligned-spots-only #end if @@ -139,7 +146,7 @@ **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. As a result you will get a single BAM (or SAM) dataset in the history. +When you type a single accession number (e.g., `SRR1582967`) into **Accession** box and click **Execute** the tool will fetch data for you. As a result you will get a single BAM (or SAM) dataset in the history. ----- @@ -154,13 +161,13 @@ .. class:: warningmark -BAM datasets produced by this option will be saved in Galaxy's history as a collection_ - a single history element containing multiple datasets. +BAM datasets produced by this option will be saved in Galaxy's history as a collection_ - a single history element containing multiple datasets. ----- **Extract data from already uploaded SRA dataset** -If a SRA dataset is present in the history, it can be converted into BAM 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 a single BAM dataset will be generated in the history. +If a SRA dataset is present in the history, it can be converted into BAM 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 a single BAM dataset will be generated in the history. @ACCESSION_LIST_HOWTO@ |
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| diff -r c38286ea7047 -r 1790dcf3c32d sra_macros.xml --- a/sra_macros.xml Wed Oct 17 11:44:12 2018 -0400 +++ b/sra_macros.xml Tue Dec 04 15:00:55 2018 -0500 |
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| @@ -15,6 +15,7 @@ <macro name="requirements"> <requirements> <requirement type="package" version="2.9.1">sra-tools</requirement> + <requirement type="package" version="1.9">samtools</requirement> </requirements> </macro> <macro name="sanitize_query"> @@ -79,7 +80,7 @@ **How to generate accession lists** 1. Go to **SRA Run Selector** by clicking this link_ - 2. Find the study you are interested in by typing a search term within the **Search** box. This can be a word (e.g., *mitochondria*) or an accession you have gotten from a paper (e.g., *SRR1582967*). + 2. Find the study you are interested in by typing a search term within the **Search** box. This can be a word (e.g., *mitochondria*) or an accession you have gotten from a paper (e.g., *SRR1582967*). 3. Once you click on the study of interest you will see the number of datasets in this study within the **Related SRA data** box 4. Click on the Runs number 5. On the page that would open you will see **Accession List** button |