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quote plus dbkeys in igv GEDAs

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This commit is contained in:
Daniel Blankenberg
2020-02-20 20:23:55 -05:00
parent 450c9b09fa
commit ef5e04d525
4 changed files with 12 additions and 12 deletions
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display_applications/igv/bam.xml
+3 -3
View File
@@ -74,9 +74,9 @@
</param>
<param type="template" name="redirect_url" strip="True" >
#if $site_id.startswith( 'local_' )
${site_link}?file=${bam_file.qp}&amp;genome=${site_organism}&amp;merge=true&amp;name=${qp( ( $bam_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
${site_link}?file=${bam_file.qp}&amp;genome=${qp($site_organism)}&amp;merge=true&amp;name=${qp( ( $bam_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
#elif $site_id.startswith( 'web_link_' ):
${site_link}?sessionURL=${bam_file.qp}&amp;genome=${site_organism}&amp;merge=true&amp;name=${qp( ( $bam_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
${site_link}?sessionURL=${bam_file.qp}&amp;genome=${qp($site_organism)}&amp;merge=true&amp;name=${qp( ( $bam_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
#else:
${jnlp.url}
#end if
@@ -86,7 +86,7 @@
<!-- Our input data table is one line per dbkey -->
<filter>${ $dataset.dbkey == $value }</filter>
<!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
<url>http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${bam_file.qp}&amp;genome=${bam_file.dbkey}&amp;merge=true&amp;name=${qp( ( $bam_file.name or $DATASET_HASH ).replace( ',', ';' ) )}</url>
<url>http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${bam_file.qp}&amp;genome=${qp($bam_file.dbkey)}&amp;merge=true&amp;name=${qp( ( $bam_file.name or $DATASET_HASH ).replace( ',', ';' ) )}</url>
<param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" />
<param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" />
</dynamic_links>
display_applications/igv/gff.xml
+3 -3
View File
@@ -73,9 +73,9 @@
</param>
<param type="template" name="redirect_url" strip="True" >
#if $site_id.startswith( 'local_' )
${site_link}?file=${gff_file.qp}&amp;genome=${site_organism}&amp;merge=true&amp;name=${qp( ( $gff_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
${site_link}?file=${gff_file.qp}&amp;genome=${qp($site_organism)}&amp;merge=true&amp;name=${qp( ( $gff_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
#elif $site_id.startswith( 'web_link_' ):
${site_link}?sessionURL=${gff_file.qp}&amp;genome=${site_organism}&amp;merge=true&amp;name=${qp( ( $gff_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
${site_link}?sessionURL=${gff_file.qp}&amp;genome=${qp($site_organism)}&amp;merge=true&amp;name=${qp( ( $gff_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
#else:
${jnlp.url}
#end if
@@ -85,7 +85,7 @@
<!-- Our input data table is one line per dbkey -->
<filter>${ $dataset.dbkey == $value }</filter>
<!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
<url>http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${gff_file.qp}&amp;genome=${gff_file.dbkey}&amp;merge=true&amp;name=${qp( ( $gff_file.name or $DATASET_HASH ).replace( ',', ';' ) )}</url>
<url>http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${gff_file.qp}&amp;genome=${qp($gff_file.dbkey)}&amp;merge=true&amp;name=${qp( ( $gff_file.name or $DATASET_HASH ).replace( ',', ';' ) )}</url>
<param type="data" name="gff_file" url="galaxy_${DATASET_HASH}.${dataset.ext}" />
</dynamic_links>
</display>
display_applications/igv/interval_as_bed.xml
+3 -3
View File
@@ -73,9 +73,9 @@
</param>
<param type="template" name="redirect_url" strip="True" >
#if $site_id.startswith( 'local_' )
${site_link}?file=${bed_file.qp}&amp;genome=${site_organism}&amp;merge=true&amp;name=${qp( ( $bed_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
${site_link}?file=${bed_file.qp}&amp;genome=${qp($site_organism)}&amp;merge=true&amp;name=${qp( ( $bed_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
#elif $site_id.startswith( 'web_link_' ):
${site_link}?sessionURL=${bed_file.qp}&amp;genome=${site_organism}&amp;merge=true&amp;name=${qp( ( $bed_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
${site_link}?sessionURL=${bed_file.qp}&amp;genome=${qp($site_organism)}&amp;merge=true&amp;name=${qp( ( $bed_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
#else:
${jnlp.url}
#end if
@@ -85,7 +85,7 @@
<!-- Our input data table is one line per dbkey -->
<filter>${ $dataset.dbkey == $value }</filter>
<!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
<url>http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${bed_file.qp}&amp;genome=${bed_file.dbkey}&amp;merge=true&amp;name=${qp( ( $bed_file.name or $DATASET_HASH ).replace( ',', ';' ) )}</url>
<url>http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${bed_file.qp}&amp;genome=${qp($bed_file.dbkey)}&amp;merge=true&amp;name=${qp( ( $bed_file.name or $DATASET_HASH ).replace( ',', ';' ) )}</url>
<param type="data" name="bed_file" url="galaxy_${DATASET_HASH}.bed" format="bedstrict" />
</dynamic_links>
</display>
display_applications/igv/vcf.xml
+3 -3
View File
@@ -74,9 +74,9 @@
</param>
<param type="template" name="redirect_url" strip="True" >
#if $site_id.startswith( 'local_' )
${site_link}?file=${bgzip_file.qp}&amp;genome=${site_organism}&amp;merge=true&amp;name=${qp( ( $bgzip_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
${site_link}?file=${bgzip_file.qp}&amp;genome=${qp($site_organism)}&amp;merge=true&amp;name=${qp( ( $bgzip_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
#elif $site_id.startswith( 'web_link_' ):
${site_link}?sessionURL=${bgzip_file.qp}&amp;genome=${site_organism}&amp;merge=true&amp;name=${qp( ( $bgzip_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
${site_link}?sessionURL=${bgzip_file.qp}&amp;genome=${qp($site_organism)}&amp;merge=true&amp;name=${qp( ( $bgzip_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
#else:
${jnlp.url}
#end if
@@ -86,7 +86,7 @@
<!-- Our input data table is one line per dbkey -->
<filter>${ $dataset.dbkey == $value }</filter>
<!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
<url>http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${bgzip_file.qp}&amp;genome=$bgzip_file.dbkey&amp;merge=true&amp;name=${qp( ( $bgzip_file.name or $DATASET_HASH ).replace( ',', ';' ) )}</url>
<url>http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${bgzip_file.qp}&amp;genome=${qp($bgzip_file.dbkey)}&amp;merge=true&amp;name=${qp( ( $bgzip_file.name or $DATASET_HASH ).replace( ',', ';' ) )}</url>
<param type="data" name="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz" format="vcf_bgzip" />
<param type="data" name="tabix_file" dataset="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz.tbi" format="tabix" />
</dynamic_links>