diff --git a/.gitattributes b/.gitattributes
new file mode 100644
index 000000000000..36b484bd26aa
--- /dev/null
+++ b/.gitattributes
@@ -0,0 +1,2 @@
+* text=auto
+lib/galaxy/datatypes/test/dosimzml eol=crlf
diff --git a/display_applications/biom/biom_simple.xml b/display_applications/biom/biom_simple.xml
index 9cf1b5256bfd..787a4b3ef4dc 100644
--- a/display_applications/biom/biom_simple.xml
+++ b/display_applications/biom/biom_simple.xml
@@ -1,7 +1,7 @@
-
-
-
- ${ url % { 'biom_file_url_qp': $biom_file.qp } }
-
-
-
+
+
+
+ ${ url % { 'biom_file_url_qp': $biom_file.qp } }
+
+
+
diff --git a/display_applications/icn3d/icn3d_simple.xml b/display_applications/icn3d/icn3d_simple.xml
index 7623130a7595..6e76c8987be6 100644
--- a/display_applications/icn3d/icn3d_simple.xml
+++ b/display_applications/icn3d/icn3d_simple.xml
@@ -1,7 +1,7 @@
-
-
-
- ${ url % { 'icn3d_file_type': $icn3d_file.ext, 'icn3d_file_url_qp': $icn3d_file.qp } }
-
-
-
+
+
+
+ ${ url % { 'icn3d_file_type': $icn3d_file.ext, 'icn3d_file_url_qp': $icn3d_file.qp } }
+
+
+
diff --git a/display_applications/igv/bam.xml b/display_applications/igv/bam.xml
index 3dcb92359f77..82a514aae841 100644
--- a/display_applications/igv/bam.xml
+++ b/display_applications/igv/bam.xml
@@ -1,94 +1,94 @@
-
-
-
-
-
-
-
-
-
-
-
- ${$site_id.startswith( 'local_' ) or $dataset.dbkey in $site_dbkeys}
-
- ${redirect_url}
-
-
-
- #if ($dataset.dbkey in $site_dbkeys)
- $site_organisms[ $site_dbkeys.index( $bam_file.dbkey ) ]
- #else:
- $bam_file.dbkey
- #end if
-
-
-
-
- IGV 1.5
- The Broad Institute
-
- IGV Software
- IGV
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- -g
- ${site_organism}
- ${bam_file.url}
-
-
-]]>
-
-
- #if $site_id.startswith( 'local_' )
- ${site_link}?file=${bam_file.qp}&genome=${site_organism}&merge=true&name=${qp( ( $bam_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
- #elif $site_id.startswith( 'web_link_' ):
- ${site_link}?sessionURL=${bam_file.qp}&genome=${site_organism}&merge=true&name=${qp( ( $bam_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
- #else:
- ${jnlp.url}
- #end if
-
-
-
-
- ${ $dataset.dbkey == $value }
-
- http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${bam_file.qp}&genome=${bam_file.dbkey}&merge=true&name=${qp( ( $bam_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+ ${$site_id.startswith( 'local_' ) or $dataset.dbkey in $site_dbkeys}
+
+ ${redirect_url}
+
+
+
+ #if ($dataset.dbkey in $site_dbkeys)
+ $site_organisms[ $site_dbkeys.index( $bam_file.dbkey ) ]
+ #else:
+ $bam_file.dbkey
+ #end if
+
+
+
+
+ IGV 1.5
+ The Broad Institute
+
+ IGV Software
+ IGV
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ -g
+ ${site_organism}
+ ${bam_file.url}
+
+
+]]>
+
+
+ #if $site_id.startswith( 'local_' )
+ ${site_link}?file=${bam_file.qp}&genome=${site_organism}&merge=true&name=${qp( ( $bam_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
+ #elif $site_id.startswith( 'web_link_' ):
+ ${site_link}?sessionURL=${bam_file.qp}&genome=${site_organism}&merge=true&name=${qp( ( $bam_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
+ #else:
+ ${jnlp.url}
+ #end if
+
+
+
+
+ ${ $dataset.dbkey == $value }
+
+ http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${bam_file.qp}&genome=${bam_file.dbkey}&merge=true&name=${qp( ( $bam_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
+
+
+
+
+
diff --git a/display_applications/igv/gff.xml b/display_applications/igv/gff.xml
index 4eabd5e578ef..78b6e6a357fa 100644
--- a/display_applications/igv/gff.xml
+++ b/display_applications/igv/gff.xml
@@ -1,92 +1,92 @@
-
-
-
-
-
-
-
-
-
-
-
- ${$site_id.startswith( 'local_' ) or $dataset.dbkey in $site_dbkeys}
-
- ${redirect_url}
-
-
- #if ($dataset.dbkey in $site_dbkeys)
- $site_organisms[ $site_dbkeys.index( $gff_file.dbkey ) ]
- #else:
- $gff_file.dbkey
- #end if
-
-
-
-
- IGV 1.5
- The Broad Institute
-
- IGV Software
- IGV
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- -g
- ${site_organism}
- ${gff_file.url}
-
-
-]]>
-
-
- #if $site_id.startswith( 'local_' )
- ${site_link}?file=${gff_file.qp}&genome=${site_organism}&merge=true&name=${qp( ( $gff_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
- #elif $site_id.startswith( 'web_link_' ):
- ${site_link}?sessionURL=${gff_file.qp}&genome=${site_organism}&merge=true&name=${qp( ( $gff_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
- #else:
- ${jnlp.url}
- #end if
-
-
-
-
- ${ $dataset.dbkey == $value }
-
- http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${gff_file.qp}&genome=${gff_file.dbkey}&merge=true&name=${qp( ( $gff_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+ ${$site_id.startswith( 'local_' ) or $dataset.dbkey in $site_dbkeys}
+
+ ${redirect_url}
+
+
+ #if ($dataset.dbkey in $site_dbkeys)
+ $site_organisms[ $site_dbkeys.index( $gff_file.dbkey ) ]
+ #else:
+ $gff_file.dbkey
+ #end if
+
+
+
+
+ IGV 1.5
+ The Broad Institute
+
+ IGV Software
+ IGV
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ -g
+ ${site_organism}
+ ${gff_file.url}
+
+
+]]>
+
+
+ #if $site_id.startswith( 'local_' )
+ ${site_link}?file=${gff_file.qp}&genome=${site_organism}&merge=true&name=${qp( ( $gff_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
+ #elif $site_id.startswith( 'web_link_' ):
+ ${site_link}?sessionURL=${gff_file.qp}&genome=${site_organism}&merge=true&name=${qp( ( $gff_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
+ #else:
+ ${jnlp.url}
+ #end if
+
+
+
+
+ ${ $dataset.dbkey == $value }
+
+ http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${gff_file.qp}&genome=${gff_file.dbkey}&merge=true&name=${qp( ( $gff_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
+
+
+
+
diff --git a/display_applications/igv/interval_as_bed.xml b/display_applications/igv/interval_as_bed.xml
index 4fd6a98095fb..aee3acc5bdf5 100644
--- a/display_applications/igv/interval_as_bed.xml
+++ b/display_applications/igv/interval_as_bed.xml
@@ -1,92 +1,92 @@
-
-
-
-
-
-
-
-
-
-
-
- ${$site_id.startswith( 'local_' ) or $dataset.dbkey in $site_dbkeys}
-
- ${redirect_url}
-
-
- #if ($dataset.dbkey in $site_dbkeys)
- $site_organisms[ $site_dbkeys.index( $bed_file.dbkey ) ]
- #else:
- $bed_file.dbkey
- #end if
-
-
-
-
- IGV 1.5
- The Broad Institute
-
- IGV Software
- IGV
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- -g
- ${site_organism}
- ${bed_file.url}
-
-
-]]>
-
-
- #if $site_id.startswith( 'local_' )
- ${site_link}?file=${bed_file.qp}&genome=${site_organism}&merge=true&name=${qp( ( $bed_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
- #elif $site_id.startswith( 'web_link_' ):
- ${site_link}?sessionURL=${bed_file.qp}&genome=${site_organism}&merge=true&name=${qp( ( $bed_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
- #else:
- ${jnlp.url}
- #end if
-
-
-
-
- ${ $dataset.dbkey == $value }
-
- http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${bed_file.qp}&genome=${bed_file.dbkey}&merge=true&name=${qp( ( $bed_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+ ${$site_id.startswith( 'local_' ) or $dataset.dbkey in $site_dbkeys}
+
+ ${redirect_url}
+
+
+ #if ($dataset.dbkey in $site_dbkeys)
+ $site_organisms[ $site_dbkeys.index( $bed_file.dbkey ) ]
+ #else:
+ $bed_file.dbkey
+ #end if
+
+
+
+
+ IGV 1.5
+ The Broad Institute
+
+ IGV Software
+ IGV
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ -g
+ ${site_organism}
+ ${bed_file.url}
+
+
+]]>
+
+
+ #if $site_id.startswith( 'local_' )
+ ${site_link}?file=${bed_file.qp}&genome=${site_organism}&merge=true&name=${qp( ( $bed_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
+ #elif $site_id.startswith( 'web_link_' ):
+ ${site_link}?sessionURL=${bed_file.qp}&genome=${site_organism}&merge=true&name=${qp( ( $bed_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
+ #else:
+ ${jnlp.url}
+ #end if
+
+
+
+
+ ${ $dataset.dbkey == $value }
+
+ http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=${bed_file.qp}&genome=${bed_file.dbkey}&merge=true&name=${qp( ( $bed_file.name or $DATASET_HASH ).replace( ',', ';' ) )}
+
+
+
+
diff --git a/display_applications/intermine/intermine_simple.xml b/display_applications/intermine/intermine_simple.xml
index 4b566ca3fd68..3bb2d58ce5ee 100644
--- a/display_applications/intermine/intermine_simple.xml
+++ b/display_applications/intermine/intermine_simple.xml
@@ -1,7 +1,7 @@
-
-
-
- ${ url % { 'intermine_file_url_qp': $intermine_file.qp } }
-
-
-
+
+
+
+ ${ url % { 'intermine_file_url_qp': $intermine_file.qp } }
+
+
+
diff --git a/display_applications/iobio/bam.xml b/display_applications/iobio/bam.xml
index 69cdabf6b427..931baedc1294 100644
--- a/display_applications/iobio/bam.xml
+++ b/display_applications/iobio/bam.xml
@@ -1,8 +1,8 @@
-
-
-
- ${url}?bam=${bam_file.qp}
-
-
-
-
+
+
+
+ ${url}?bam=${bam_file.qp}
+
+
+
+
diff --git a/scripts/microbes/README.txt b/scripts/microbes/README.txt
index 7904f20d09d6..1f1abecad269 100644
--- a/scripts/microbes/README.txt
+++ b/scripts/microbes/README.txt
@@ -1,24 +1,24 @@
-The Scripts found in this directory are used to download and generate the files relating to Galaxy as a Microbial Resource.
-This includes scripts to access the NCBI Genome Projects site, download relevent data, and convert to a form usable in Galaxy. Data is generated for the Microbial Datasource Tool, as well as for Galaxy Interval Operations (chromosome names and lengths), and also the extract Genomic DNA tool. Information about organisms is also written into '.info' files found in each organism directory.
-
-Step 3 requires a binary 'faToNib' to properly generate sequence files.
-
-Steps should be performed in the order they appear here.
-
-(1.) To Download and process Genome Projects from NCBI into a form usable by Galaxy:
- python /GALAXY_ROOT/scripts/microbes/harvest_bacteria.py /OUTPUT/DIRECTORY/microbes/ > /OUTPUT/DIRECTORY/harvest.txt
-
-(2.) To Walk downloaded Genome Projects and Convert, in place, IDs to match the UCSC Archaea browser, where applicable:
- python /GALAXY_ROOT/scripts/microbes/ncbi_to_ucsc.py /OUTPUT/DIRECTORY/microbes/ > /OUTPUT/DIRECTORY/ncbi_to_ucsc.txt
-
-(3.) To create nib files (for extraction) and to generate the location file content for Microbes used for extracting Genomic DNA:
- python /GALAXY_ROOT/scripts/microbes/create_nib_seq_loc_file.py /OUTPUT/DIRECTORY/microbes/ seq.loc > /OUTPUT/DIRECTORY/sequence.txt
-
-(4.) To create the location file for the Microbial Data Resource tool in Galaxy:
- python /GALAXY_ROOT/scripts/microbes/create_bacteria_loc_file.py /OUTPUT/DIRECTORY/microbes/ > /OUTPUT/DIRECTORY/microbial_data.loc
-
-(5.) To Generate a single file containing the lengths for each chromosome for each species, to be added to 'manual_builds.txt':
- python /GALAXY_ROOT/scripts/microbes/get_builds_lengths.py /OUTPUT/DIRECTORY/microbes/ > /OUTPUT/DIRECTORY/microbes.len
-
-(6.) To Create the Wiki Table listing available Microbial Data in Galaxy:
+The Scripts found in this directory are used to download and generate the files relating to Galaxy as a Microbial Resource.
+This includes scripts to access the NCBI Genome Projects site, download relevent data, and convert to a form usable in Galaxy. Data is generated for the Microbial Datasource Tool, as well as for Galaxy Interval Operations (chromosome names and lengths), and also the extract Genomic DNA tool. Information about organisms is also written into '.info' files found in each organism directory.
+
+Step 3 requires a binary 'faToNib' to properly generate sequence files.
+
+Steps should be performed in the order they appear here.
+
+(1.) To Download and process Genome Projects from NCBI into a form usable by Galaxy:
+ python /GALAXY_ROOT/scripts/microbes/harvest_bacteria.py /OUTPUT/DIRECTORY/microbes/ > /OUTPUT/DIRECTORY/harvest.txt
+
+(2.) To Walk downloaded Genome Projects and Convert, in place, IDs to match the UCSC Archaea browser, where applicable:
+ python /GALAXY_ROOT/scripts/microbes/ncbi_to_ucsc.py /OUTPUT/DIRECTORY/microbes/ > /OUTPUT/DIRECTORY/ncbi_to_ucsc.txt
+
+(3.) To create nib files (for extraction) and to generate the location file content for Microbes used for extracting Genomic DNA:
+ python /GALAXY_ROOT/scripts/microbes/create_nib_seq_loc_file.py /OUTPUT/DIRECTORY/microbes/ seq.loc > /OUTPUT/DIRECTORY/sequence.txt
+
+(4.) To create the location file for the Microbial Data Resource tool in Galaxy:
+ python /GALAXY_ROOT/scripts/microbes/create_bacteria_loc_file.py /OUTPUT/DIRECTORY/microbes/ > /OUTPUT/DIRECTORY/microbial_data.loc
+
+(5.) To Generate a single file containing the lengths for each chromosome for each species, to be added to 'manual_builds.txt':
+ python /GALAXY_ROOT/scripts/microbes/get_builds_lengths.py /OUTPUT/DIRECTORY/microbes/ > /OUTPUT/DIRECTORY/microbes.len
+
+(6.) To Create the Wiki Table listing available Microbial Data in Galaxy:
python /GALAXY_ROOT/scripts/microbes/create_bacteria_table.py /OUTPUT/DIRECTORY/microbes/ > /OUTPUT/DIRECTORY/microbes.table
\ No newline at end of file
diff --git a/test/functional/tools/catDocker.xml b/test/functional/tools/catDocker.xml
index 1437ebb717b1..470fef9ccf09 100644
--- a/test/functional/tools/catDocker.xml
+++ b/test/functional/tools/catDocker.xml
@@ -1,28 +1,28 @@
-
- tail-to-head
-
- busybox:ubuntu-14.04
-
-
- echo "Galaxy slots passed through contain as \$GALAXY_SLOTS";
- cat $input1
- #for $q in $queries
- ${q.input2}
- #end for
- > $out_file1;
- echo "Work dir output" > working_file
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+ tail-to-head
+
+ busybox:ubuntu-14.04
+
+
+ echo "Galaxy slots passed through contain as \$GALAXY_SLOTS";
+ cat $input1
+ #for $q in $queries
+ ${q.input2}
+ #end for
+ > $out_file1;
+ echo "Work dir output" > working_file
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/test/functional/tools/for_workflows/cat.xml b/test/functional/tools/for_workflows/cat.xml
index 19016e35d77e..850469141fdc 100644
--- a/test/functional/tools/for_workflows/cat.xml
+++ b/test/functional/tools/for_workflows/cat.xml
@@ -1,19 +1,19 @@
-
- tail-to-head
-
- cat $input1 #for $q in $queries# ${q.input2} #end for# > $out_file1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+ tail-to-head
+
+ cat $input1 #for $q in $queries# ${q.input2} #end for# > $out_file1
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/test/shed_functional/test_data/filtering/readme.txt b/test/shed_functional/test_data/filtering/readme.txt
index 9ad35df358ce..291b190d703b 100644
--- a/test/shed_functional/test_data/filtering/readme.txt
+++ b/test/shed_functional/test_data/filtering/readme.txt
@@ -1,2 +1,2 @@
-These characters should not result in a unicode decoding error:
+These characters should not result in a unicode decoding error:
....
\ No newline at end of file