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comparison sam_dump.xml @ 14:1790dcf3c32d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 30ec06de1f3056967f5cc2d8ef57f9692d5533d7
author iuc
date Tue, 04 Dec 2018 15:00:55 -0500
parents c38286ea7047
children aad3885b3216
comparison
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13:c38286ea7047 14:1790dcf3c32d
1 <tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@.3"> 1 <tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@.4">
2 <description>format from NCBI SRA</description> 2 <description>format from NCBI SRA</description>
3 <macros> 3 <macros>
4 <import>sra_macros.xml</import> 4 <import>sra_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
15 export HOME=\$PWD && 15 export HOME=\$PWD &&
16 vdb-config --restore-defaults && 16 vdb-config --restore-defaults &&
17 vdb-config -s "/repository/user/main/public/root=\$PWD" && 17 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
18 ## Do not use prefetch if region is specified, to avoid downloading 18 ## Do not use prefetch if region is specified, to avoid downloading
19 ## the complete sra file. 19 ## the complete sra file.
20 #if ( str( $adv.region ) == "" ): 20
21 ASCP_PATH=`command -v ascp` && 21 #if $input.input_select == "file":
22 ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true && 22 sam-dump --log-level fatal '${input.file.name}'
23 prefetch -X 200G --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "\$acc" && 23 #else:
24 ## Duplicate vdb-config, in case settings changed between prefetch and 24 #if ( str( $adv.region ) == "" ):
25 ## dump command. 25 ASCP_PATH=`command -v ascp` &&
26 vdb-config -s "/repository/user/main/public/root=\$PWD" && 26 ASCP_KEY=`dirname \$ASCP_PATH`/asperaweb_id_dsa.openssh || true &&
27 prefetch -X 200G --ascp-path "\$ASCP_PATH|\$ASCP_KEY" "\$acc" &&
28 ## Duplicate vdb-config, in case settings changed between prefetch and
29 ## dump command.
30 vdb-config -s "/repository/user/main/public/root=\$PWD" &&
31 #end if
32 sam-dump --log-level fatal --disable-multithreading
27 #end if 33 #end if
28 sam-dump --log-level fatal --disable-multithreading 34
29 #if str( $adv.region ) != "": 35 #if str( $adv.region ) != "":
30 --aligned-region '$adv.region' 36 --aligned-region '$adv.region'
31 #end if 37 #end if
32 #if str( $adv.matepairDist ) != "": 38 #if str( $adv.matepairDist ) != "":
33 --matepair-distance '$adv.matepairDist' 39 --matepair-distance '$adv.matepairDist'
37 #end if 43 #end if
38 --header 44 --header
39 #if str( $adv.alignments ) == "both": 45 #if str( $adv.alignments ) == "both":
40 --unaligned 46 --unaligned
41 #end if 47 #end if
48
42 #if str( $adv.alignments ) == "unaligned": 49 #if str( $adv.alignments ) == "unaligned":
43 --unaligned-spots-only 50 --unaligned-spots-only
44 #end if 51 #end if
45 #if (str( $adv.primary ) == "yes") and (str ( $adv.alignments != "unaligned") ): 52 #if (str( $adv.primary ) == "yes") and (str ( $adv.alignments != "unaligned") ):
46 --primary 53 --primary
137 144
138 ------ 145 ------
139 146
140 **Uploading data for a single accession** 147 **Uploading data for a single accession**
141 148
142 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. 149 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.
143 150
144 ----- 151 -----
145 152
146 **Uploading multiple datasets using a list of accessions** 153 **Uploading multiple datasets using a list of accessions**
147 154
152 3. Choose uploaded file within the **sra accession list** field 159 3. Choose uploaded file within the **sra accession list** field
153 4. Click **Execute** 160 4. Click **Execute**
154 161
155 .. class:: warningmark 162 .. class:: warningmark
156 163
157 BAM datasets produced by this option will be saved in Galaxy's history as a collection_ - a single history element containing multiple datasets. 164 BAM datasets produced by this option will be saved in Galaxy's history as a collection_ - a single history element containing multiple datasets.
158 165
159 ----- 166 -----
160 167
161 **Extract data from already uploaded SRA dataset** 168 **Extract data from already uploaded SRA dataset**
162 169
163 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. 170 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.
164 171
165 @ACCESSION_LIST_HOWTO@ 172 @ACCESSION_LIST_HOWTO@
166 173
167 ----- 174 -----
168 175