diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py index c2919f75500..66f737565b2 100755 --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -8,6 +8,7 @@ pkg_resources.require( "simplejson" ) import logging, os, string, sys, tempfile, glob, shutil, types, urllib, subprocess, random, math, traceback import simplejson import binascii +from mako.template import Template from UserDict import DictMixin from galaxy.util.odict import odict from galaxy.util.bunch import Bunch @@ -1068,7 +1069,8 @@ class Tool: break def parse_help( self, root ): """ - Parse the help text for the tool. Formatted in reStructuredText. + Parse the help text for the tool. Formatted in reStructuredText, but + stored as Mako to allow for dynamic image paths. This implementation supports multiple pages. """ # TODO: Allow raw HTML or an external link. @@ -1080,7 +1082,7 @@ class Tool: help_pages = self.help.findall( "page" ) help_header = self.help.text try: - self.help = util.rst_to_html(self.help.text) + self.help = Template( util.rst_to_html(self.help.text) ) except: log.exception( "error in help for tool %s" % self.name ) # Multiple help page case @@ -1090,7 +1092,7 @@ class Tool: help_footer = help_footer + help_page.tail # Each page has to rendered all-together because of backreferences allowed by rst try: - self.help_by_page = [ util.rst_to_html( help_header + x + help_footer ) + self.help_by_page = [ Template( util.rst_to_html( help_header + x + help_footer ) ) for x in self.help_by_page ] except: log.exception( "error in multi-page help for tool %s" % self.name ) diff --git a/templates/tool_form.mako b/templates/tool_form.mako index 69e8c665959..25068f511d5 100644 --- a/templates/tool_form.mako +++ b/templates/tool_form.mako @@ -332,6 +332,9 @@ else: tool_help = tool.help + # Help is Mako template, so render using current static path. + tool_help = tool_help.render( static_path=h.url_for( '/static' ) ) + # Convert to unicode to display non-ascii characters. if type( tool_help ) is not unicode: tool_help = unicode( tool_help, 'utf-8') diff --git a/tools/discreteWavelet/execute_dwt_IvC_all.xml b/tools/discreteWavelet/execute_dwt_IvC_all.xml index fb048e582bb..794f82ceb9b 100644 --- a/tools/discreteWavelet/execute_dwt_IvC_all.xml +++ b/tools/discreteWavelet/execute_dwt_IvC_all.xml @@ -101,11 +101,11 @@ The first output file:: The second output file: -.. image:: ./static/operation_icons/dwt_IvC_1.png -.. image:: ./static/operation_icons/dwt_IvC_2.png -.. image:: ./static/operation_icons/dwt_IvC_3.png -.. image:: ./static/operation_icons/dwt_IvC_4.png -.. image:: ./static/operation_icons/dwt_IvC_5.png +.. image:: ${static_path}/operation_icons/dwt_IvC_1.png +.. image:: ${static_path}/operation_icons/dwt_IvC_2.png +.. image:: ${static_path}/operation_icons/dwt_IvC_3.png +.. image:: ${static_path}/operation_icons/dwt_IvC_4.png +.. image:: ${static_path}/operation_icons/dwt_IvC_5.png diff --git a/tools/discreteWavelet/execute_dwt_cor_aVa_perClass.xml b/tools/discreteWavelet/execute_dwt_cor_aVa_perClass.xml index 23c90b4b035..dfd285d6d23 100644 --- a/tools/discreteWavelet/execute_dwt_cor_aVa_perClass.xml +++ b/tools/discreteWavelet/execute_dwt_cor_aVa_perClass.xml @@ -101,11 +101,11 @@ The first output file:: The second output file: -.. image:: ./static/operation_icons/dwt_cor_aVa_1.png -.. image:: ./static/operation_icons/dwt_cor_aVa_2.png -.. image:: ./static/operation_icons/dwt_cor_aVa_3.png -.. image:: ./static/operation_icons/dwt_cor_aVa_4.png -.. image:: ./static/operation_icons/dwt_cor_aVa_5.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVa_1.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVa_2.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVa_3.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVa_4.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVa_5.png diff --git a/tools/discreteWavelet/execute_dwt_cor_aVb_all.xml b/tools/discreteWavelet/execute_dwt_cor_aVb_all.xml index 99147015a84..8575b27be88 100644 --- a/tools/discreteWavelet/execute_dwt_cor_aVb_all.xml +++ b/tools/discreteWavelet/execute_dwt_cor_aVb_all.xml @@ -106,16 +106,16 @@ The first output file:: The second output file: -.. image:: ./static/operation_icons/dwt_cor_aVb_all_1.png -.. image:: ./static/operation_icons/dwt_cor_aVb_all_2.png -.. image:: ./static/operation_icons/dwt_cor_aVb_all_3.png -.. image:: ./static/operation_icons/dwt_cor_aVb_all_4.png -.. image:: ./static/operation_icons/dwt_cor_aVb_all_5.png -.. image:: ./static/operation_icons/dwt_cor_aVb_all_6.png -.. image:: ./static/operation_icons/dwt_cor_aVb_all_7.png -.. image:: ./static/operation_icons/dwt_cor_aVb_all_8.png -.. image:: ./static/operation_icons/dwt_cor_aVb_all_9.png -.. image:: ./static/operation_icons/dwt_cor_aVb_all_10.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_1.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_2.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_3.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_4.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_5.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_6.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_7.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_8.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_9.png +.. image:: ${static_path}/operation_icons/dwt_cor_aVb_all_10.png diff --git a/tools/discreteWavelet/execute_dwt_var_perClass.xml b/tools/discreteWavelet/execute_dwt_var_perClass.xml index 22fa0ad6257..0656f43da97 100644 --- a/tools/discreteWavelet/execute_dwt_var_perClass.xml +++ b/tools/discreteWavelet/execute_dwt_var_perClass.xml @@ -98,7 +98,7 @@ The second output file:: The third output file: -.. image:: ./static/operation_icons/dwt_var_perClass.png +.. image:: ${static_path}/operation_icons/dwt_var_perClass.png diff --git a/tools/evolution/add_scores.xml b/tools/evolution/add_scores.xml index ffa6ecac433..c7616b3d238 100644 --- a/tools/evolution/add_scores.xml +++ b/tools/evolution/add_scores.xml @@ -43,8 +43,8 @@ This currently works only for builds hg18 and hg19. The input can be any interval_ format dataset. The output is also in interval format. (`Dataset missing?`_) -.. _interval: ./static/formatHelp.html#interval -.. _Dataset missing?: ./static/formatHelp.html +.. _interval: ${static_path}/formatHelp.html#interval +.. _Dataset missing?: ${static_path}/formatHelp.html ----- diff --git a/tools/evolution/codingSnps.xml b/tools/evolution/codingSnps.xml index bae3fc386e8..bd9e346fe10 100644 --- a/tools/evolution/codingSnps.xml +++ b/tools/evolution/codingSnps.xml @@ -94,9 +94,9 @@ The SNP dataset is in interval_ format, with a column of SNPs as described below The gene dataset is in BED_ format with 12 columns. The output dataset is also interval. (`Dataset missing?`_) -.. _interval: ./static/formatHelp.html#interval -.. _BED: ./static/formatHelp.html#bed -.. _Dataset missing?: ./static/formatHelp.html +.. _interval: ${static_path}/formatHelp.html#interval +.. _BED: ${static_path}/formatHelp.html#bed +.. _Dataset missing?: ${static_path}/formatHelp.html ----- diff --git a/tools/fastx_toolkit/fasta_clipping_histogram.xml b/tools/fastx_toolkit/fasta_clipping_histogram.xml index 5294f40a2b0..859cc6317b5 100644 --- a/tools/fastx_toolkit/fasta_clipping_histogram.xml +++ b/tools/fastx_toolkit/fasta_clipping_histogram.xml @@ -1,6 +1,6 @@ chart - fastx_toolkit + fastx_toolkit fasta_clipping_histogram.pl $input $outfile @@ -25,13 +25,13 @@ This tool creates a histogram image of sequence lengths distribution in a given In the following library, most sequences are 24-mers to 27-mers. This could indicate an abundance of endo-siRNAs (depending of course of what you've tried to sequence in the first place). -.. image:: ./static/fastx_icons/fasta_clipping_histogram_1.png +.. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_1.png In the following library, most sequences are 19,22 or 23-mers. This could indicate an abundance of miRNAs (depending of course of what you've tried to sequence in the first place). -.. image:: ./static/fastx_icons/fasta_clipping_histogram_2.png +.. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_2.png ----- @@ -81,7 +81,7 @@ Example 1 - The following FASTA file *does not* have multiplicity counts:: Each sequence is counts as one, to produce the following chart: -.. image:: ./static/fastx_icons/fasta_clipping_histogram_3.png +.. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_3.png Example 2 - The following FASTA file have multiplicity counts:: @@ -95,7 +95,7 @@ Example 2 - The following FASTA file have multiplicity counts:: The first sequence counts as 2, the second as 10, the third as 3, to produce the following chart: -.. image:: ./static/fastx_icons/fasta_clipping_histogram_4.png +.. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_4.png Use the **FASTA Collapser** tool to create FASTA files with multiplicity counts. diff --git a/tools/fastx_toolkit/fastq_quality_boxplot.xml b/tools/fastx_toolkit/fastq_quality_boxplot.xml index 14241b39285..77e9d0896ac 100644 --- a/tools/fastx_toolkit/fastq_quality_boxplot.xml +++ b/tools/fastx_toolkit/fastq_quality_boxplot.xml @@ -32,16 +32,16 @@ Creates a boxplot graph for the quality scores in the library. An excellent quality library (median quality is 40 for almost all 36 cycles): -.. image:: ./static/fastx_icons/fastq_quality_boxplot_1.png +.. image:: ${static_path}/fastx_icons/fastq_quality_boxplot_1.png A relatively good quality library (median quality degrades towards later cycles): -.. image:: ./static/fastx_icons/fastq_quality_boxplot_2.png +.. image:: ${static_path}/fastx_icons/fastq_quality_boxplot_2.png A low quality library (median drops quickly): -.. image:: ./static/fastx_icons/fastq_quality_boxplot_3.png +.. image:: ${static_path}/fastx_icons/fastq_quality_boxplot_3.png ------ diff --git a/tools/fastx_toolkit/fastx_barcode_splitter.xml b/tools/fastx_toolkit/fastx_barcode_splitter.xml index a3873054ae0..e9251d7425e 100644 --- a/tools/fastx_toolkit/fastx_barcode_splitter.xml +++ b/tools/fastx_toolkit/fastx_barcode_splitter.xml @@ -1,6 +1,6 @@ - fastx_toolkit + fastx_toolkit fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "$input.name" "$output.files_path" --mismatches $mismatches --partial $partial $EOL > $output @@ -62,7 +62,7 @@ The output of this tool is an HTML file, displaying the split counts and the fil **Output Example** -.. image:: ./static/fastx_icons/barcode_splitter_output_example.png +.. image:: ${static_path}/fastx_icons/barcode_splitter_output_example.png ------ diff --git a/tools/fastx_toolkit/fastx_clipper.xml b/tools/fastx_toolkit/fastx_clipper.xml index 90c4f6db1ab..98a7a661735 100644 --- a/tools/fastx_toolkit/fastx_clipper.xml +++ b/tools/fastx_toolkit/fastx_clipper.xml @@ -1,6 +1,6 @@ adapter sequences - fastx_toolkit + fastx_toolkit zcat -f $input | fastx_clipper -l $minlength -a $clip_source.clip_sequence -d $keepdelta -o $output -v $KEEP_N $DISCARD_OPTIONS #if $input.ext == "fastqsanger": @@ -82,7 +82,7 @@ This tool clips adapters from the 3'-end of the sequences in a FASTA/FASTQ file. **Clipping Illustration:** -.. image:: ./static/fastx_icons/fastx_clipper_illustration.png +.. image:: ${static_path}/fastx_icons/fastx_clipper_illustration.png @@ -93,7 +93,7 @@ This tool clips adapters from the 3'-end of the sequences in a FASTA/FASTQ file. **Clipping Example:** -.. image:: ./static/fastx_icons/fastx_clipper_example.png +.. image:: ${static_path}/fastx_icons/fastx_clipper_example.png diff --git a/tools/fastx_toolkit/fastx_nucleotides_distribution.xml b/tools/fastx_toolkit/fastx_nucleotides_distribution.xml index 29254e47ce7..7ed2f93c61f 100644 --- a/tools/fastx_toolkit/fastx_nucleotides_distribution.xml +++ b/tools/fastx_toolkit/fastx_nucleotides_distribution.xml @@ -1,6 +1,6 @@ - fastx_toolkit + fastx_toolkit fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o $output @@ -26,19 +26,19 @@ Creates a stacked-histogram graph for the nucleotide distribution in the Solexa The following chart clearly shows the barcode used at the 5'-end of the library: **GATCT** -.. image:: ./static/fastx_icons/fastq_nucleotides_distribution_1.png +.. image:: ${static_path}/fastx_icons/fastq_nucleotides_distribution_1.png In the following chart, one can almost 'read' the most abundant sequence by looking at the dominant values: **TGATA TCGTA TTGAT GACTG AA...** -.. image:: ./static/fastx_icons/fastq_nucleotides_distribution_2.png +.. image:: ${static_path}/fastx_icons/fastq_nucleotides_distribution_2.png The following chart shows a growing number of unknown (N) nucleotides towards later cycles (which might indicate a sequencing problem): -.. image:: ./static/fastx_icons/fastq_nucleotides_distribution_3.png +.. image:: ${static_path}/fastx_icons/fastq_nucleotides_distribution_3.png But most of the time, the chart will look rather random: -.. image:: ./static/fastx_icons/fastq_nucleotides_distribution_4.png +.. image:: ${static_path}/fastx_icons/fastq_nucleotides_distribution_4.png ------ diff --git a/tools/maf/interval2maf.xml b/tools/maf/interval2maf.xml index 44eaf40b529..76783e92238 100644 --- a/tools/maf/interval2maf.xml +++ b/tools/maf/interval2maf.xml @@ -110,7 +110,7 @@ This tool takes genomic coordinates, superimposes them on multiple alignments (i Here a single interval is superimposed on three MAF blocks. Blocks 1 and 3 are trimmed because they extend beyond boundaries of the interval: -.. image:: ./static/images/maf_icons/interval2maf.png +.. image:: ${static_path}/images/maf_icons/interval2maf.png ------- diff --git a/tools/maf/interval2maf_pairwise.xml b/tools/maf/interval2maf_pairwise.xml index 7cfbb104c2e..83762e94d8f 100644 --- a/tools/maf/interval2maf_pairwise.xml +++ b/tools/maf/interval2maf_pairwise.xml @@ -37,7 +37,7 @@ This tool takes genomic coordinates, superimposes them on pairwise alignments (i Here a single interval is superimposed on three MAF blocks. Blocks 1 and 3 are trimmed because they extend beyond boundaries of the interval: -.. image:: ./static/images/maf_icons/interval2maf.png +.. image:: ${static_path}/images/maf_icons/interval2maf.png ------ diff --git a/tools/maf/interval_maf_to_merged_fasta.xml b/tools/maf/interval_maf_to_merged_fasta.xml index de299158f6d..4727ace907f 100644 --- a/tools/maf/interval_maf_to_merged_fasta.xml +++ b/tools/maf/interval_maf_to_merged_fasta.xml @@ -101,7 +101,7 @@ A single genomic region can be covered by multiple alignment blocks. In many cas Here three MAF blocks overlapping a single interval are stitched together. Space between blocks 2 and 3 is filled with gaps: -.. image:: ./static/images/maf_icons/stitchMaf.png +.. image:: ${static_path}/images/maf_icons/stitchMaf.png ------ diff --git a/tools/metag_tools/blat_mapping.xml b/tools/metag_tools/blat_mapping.xml index 1af82c3149a..c8b1ea0badc 100644 --- a/tools/metag_tools/blat_mapping.xml +++ b/tools/metag_tools/blat_mapping.xml @@ -35,7 +35,7 @@ Showing reads coverage on human chromosome 22 (partial result) in UCSC Genome Browser Custom Track: - .. image:: ./static/images/blat_mapping_example.png + .. image:: ${static_path}/images/blat_mapping_example.png :width: 600 diff --git a/tools/metag_tools/convert_SOLiD_color2nuc.xml b/tools/metag_tools/convert_SOLiD_color2nuc.xml index ddcbcf93975..5701b9f51cf 100644 --- a/tools/metag_tools/convert_SOLiD_color2nuc.xml +++ b/tools/metag_tools/convert_SOLiD_color2nuc.xml @@ -65,7 +65,7 @@ This tool converts a color space sequence to nucleotides. The leading character Each di-nucleotide is represented by a single digit: 0 to 3. The matrix is symmetric, thus the leading nucleotide is necessary to determine the sequence (otherwise there are four possibilities). - .. image:: ./static/images/dualcolorcode.png + .. image:: ${static_path}/images/dualcolorcode.png diff --git a/tools/metag_tools/short_reads_figure_score.xml b/tools/metag_tools/short_reads_figure_score.xml index 8b791c8e905..df7c80dae09 100644 --- a/tools/metag_tools/short_reads_figure_score.xml +++ b/tools/metag_tools/short_reads_figure_score.xml @@ -56,7 +56,7 @@ Illumina (Solexa) data:: Quality scores are summarized as boxplot (Roche 454 FLX data): -.. image:: ./static/images/short_reads_boxplot.png +.. image:: ${static_path}/images/short_reads_boxplot.png where the **X-axis** is coordinate along the read and the **Y-axis** is quality score adjusted to comply with the Phred score metric. Units on the X-axis depend on whether your data comes from Roche (454) or Illumina (Solexa) and ABI SOLiD machines: diff --git a/tools/mutation/visualize.xml b/tools/mutation/visualize.xml index 90ae83fcfe9..4c1a5455c84 100644 --- a/tools/mutation/visualize.xml +++ b/tools/mutation/visualize.xml @@ -96,7 +96,7 @@ To visualize the two samples in the input file, the following parameters are sel Visualization output: -.. image:: ./static/images/mutation_visualization_example.png +.. image:: ${static_path}/images/mutation_visualization_example.png :width: 150 Here the left-most column represents the position and the background color is the reference base color. Each column on its right describe each sample. diff --git a/tools/new_operations/basecoverage.xml b/tools/new_operations/basecoverage.xml index 9bbdd50d3b7..19161a5f423 100644 --- a/tools/new_operations/basecoverage.xml +++ b/tools/new_operations/basecoverage.xml @@ -38,7 +38,7 @@ See Galaxy Interval Operation Screencasts_ (right click to open this link in ano **Example** -.. image:: ./static/operation_icons/gops_baseCoverage.gif +.. image:: ${static_path}/operation_icons/gops_baseCoverage.gif diff --git a/tools/new_operations/cluster.xml b/tools/new_operations/cluster.xml index 06a88987d36..24bedd46f25 100644 --- a/tools/new_operations/cluster.xml +++ b/tools/new_operations/cluster.xml @@ -86,11 +86,11 @@ See Galaxy Interval Operation Screencasts_ (right click to open this link in ano Find Clusters: -.. image:: ./static/operation_icons/gops_clusterFind.gif +.. image:: ${static_path}/operation_icons/gops_clusterFind.gif Merge Clusters: -.. image:: ./static/operation_icons/gops_clusterMerge.gif +.. image:: ${static_path}/operation_icons/gops_clusterMerge.gif diff --git a/tools/new_operations/complement.xml b/tools/new_operations/complement.xml index b7f6492775d..664aa30a288 100644 --- a/tools/new_operations/complement.xml +++ b/tools/new_operations/complement.xml @@ -55,7 +55,7 @@ See Galaxy Interval Operation Screencasts_ (right click to open this link in ano **Example** -.. image:: ./static/operation_icons/gops_complement.gif +.. image:: ${static_path}/operation_icons/gops_complement.gif diff --git a/tools/new_operations/concat.xml b/tools/new_operations/concat.xml index 34acaf5f8c8..dc33affd1da 100644 --- a/tools/new_operations/concat.xml +++ b/tools/new_operations/concat.xml @@ -53,7 +53,7 @@ See Galaxy Interval Operation Screencasts_ (right click to open this link in ano **Example** -.. image:: ./static/operation_icons/gops_concatenate.gif +.. image:: ${static_path}/operation_icons/gops_concatenate.gif \ No newline at end of file diff --git a/tools/new_operations/get_flanks.xml b/tools/new_operations/get_flanks.xml index 1c9cb4d29b7..3a9c29efcd6 100644 --- a/tools/new_operations/get_flanks.xml +++ b/tools/new_operations/get_flanks.xml @@ -58,7 +58,7 @@ This tool finds the upstream and/or downstream flanking region(s) of all the sel chr22 500 800 NM_174568 0 + -.. image:: ./static/operation_icons/flanks_ex1.gif +.. image:: ${static_path}/operation_icons/flanks_ex1.gif **Example 2** @@ -70,7 +70,7 @@ This tool finds the upstream and/or downstream flanking region(s) of all the sel chr22 500 800 NM_028946 0 - -.. image:: ./static/operation_icons/flanks_ex2.gif +.. image:: ${static_path}/operation_icons/flanks_ex2.gif diff --git a/tools/new_operations/intersect.xml b/tools/new_operations/intersect.xml index 75e3750f9f9..642a94d34cd 100644 --- a/tools/new_operations/intersect.xml +++ b/tools/new_operations/intersect.xml @@ -133,11 +133,11 @@ See Galaxy Interval Operation Screencasts_ (right click to open this link in ano Overlapping Intervals: -.. image:: ./static/operation_icons/gops_intersectOverlappingIntervals.gif +.. image:: ${static_path}/operation_icons/gops_intersectOverlappingIntervals.gif Overlapping Pieces of Intervals: -.. image:: ./static/operation_icons/gops_intersectOverlappingPieces.gif +.. image:: ${static_path}/operation_icons/gops_intersectOverlappingPieces.gif diff --git a/tools/new_operations/join.xml b/tools/new_operations/join.xml index 257887342de..4d5331ec995 100644 --- a/tools/new_operations/join.xml +++ b/tools/new_operations/join.xml @@ -94,23 +94,23 @@ See Galaxy Interval Operation Screencasts_ (right click to open this link in ano **Examples** -.. image:: ./static/operation_icons/gops_joinRecordsList.gif +.. image:: ${static_path}/operation_icons/gops_joinRecordsList.gif Only records that are joined (inner join): -.. image:: ./static/operation_icons/gops_joinInner.gif +.. image:: ${static_path}/operation_icons/gops_joinInner.gif All records of first dataset: -.. image:: ./static/operation_icons/gops_joinLeftOuter.gif +.. image:: ${static_path}/operation_icons/gops_joinLeftOuter.gif All records of second dataset: -.. image:: ./static/operation_icons/gops_joinRightOuter.gif +.. image:: ${static_path}/operation_icons/gops_joinRightOuter.gif All records of both datasets: -.. image:: ./static/operation_icons/gops_joinFullOuter.gif +.. image:: ${static_path}/operation_icons/gops_joinFullOuter.gif diff --git a/tools/new_operations/merge.xml b/tools/new_operations/merge.xml index e5a79196c2c..33c2abc096f 100644 --- a/tools/new_operations/merge.xml +++ b/tools/new_operations/merge.xml @@ -52,7 +52,7 @@ This operation merges all overlapping intervals into single intervals. **Example** -.. image:: ./static/operation_icons/gops_merge.gif +.. image:: ${static_path}/operation_icons/gops_merge.gif \ No newline at end of file diff --git a/tools/new_operations/subtract.xml b/tools/new_operations/subtract.xml index 2aca5de5010..9ab69748252 100644 --- a/tools/new_operations/subtract.xml +++ b/tools/new_operations/subtract.xml @@ -114,11 +114,11 @@ See Galaxy Interval Operation Screencasts_ (right click to open this link in ano Intervals with no overlap: -.. image:: ./static/operation_icons/gops_subtractOverlappingIntervals.gif +.. image:: ${static_path}/operation_icons/gops_subtractOverlappingIntervals.gif Non-overlapping pieces of intervals: -.. image:: ./static/operation_icons/gops_subtractOverlappingPieces.gif +.. image:: ${static_path}/operation_icons/gops_subtractOverlappingPieces.gif diff --git a/tools/ngs_simulation/ngs_simulation.xml b/tools/ngs_simulation/ngs_simulation.xml index 080f047be57..596b88ee04b 100644 --- a/tools/ngs_simulation/ngs_simulation.xml +++ b/tools/ngs_simulation/ngs_simulation.xml @@ -188,7 +188,7 @@ There are one or two. The first is a png that contains two different plots and i Plot output (png): -.. image:: ./static/images/ngs_simulation.png +.. image:: ${static_path}/images/ngs_simulation.png Summary output (txt):: diff --git a/tools/phenotype_association/beam.xml b/tools/phenotype_association/beam.xml index 9c5302fdec2..c8d3930bd2e 100644 --- a/tools/phenotype_association/beam.xml +++ b/tools/phenotype_association/beam.xml @@ -59,9 +59,9 @@ single-SNP associations), please use the GPASS tool instead.** The input dataset must be in lped_ format. The output datasets are both tabular_. (`Dataset missing?`_) -.. _lped: ./static/formatHelp.html#lped -.. _tabular: ./static/formatHelp.html#tabular -.. _Dataset missing?: ./static/formatHelp.html +.. _lped: ${static_path}/formatHelp.html#lped +.. _tabular: ${static_path}/formatHelp.html#tabular +.. _Dataset missing?: ${static_path}/formatHelp.html ----- diff --git a/tools/phenotype_association/ctd.xml b/tools/phenotype_association/ctd.xml index 345adabdff5..b769758b96c 100644 --- a/tools/phenotype_association/ctd.xml +++ b/tools/phenotype_association/ctd.xml @@ -246,7 +246,7 @@ either the general interaction type or a more specific one. Home page: http://ctdbase.org -.. _tabular: ./static/formatHelp.html#tab +.. _tabular: ${static_path}/formatHelp.html#tab ----- diff --git a/tools/phenotype_association/funDo.xml b/tools/phenotype_association/funDo.xml index 22277f066b6..113355ea046 100644 --- a/tools/phenotype_association/funDo.xml +++ b/tools/phenotype_association/funDo.xml @@ -34,7 +34,7 @@ There is no input dataset. The output is in interval_ format. -.. _interval: ./static/formatHelp.html#interval +.. _interval: ${static_path}/formatHelp.html#interval ----- diff --git a/tools/phenotype_association/gpass.xml b/tools/phenotype_association/gpass.xml index 831b380de8e..231a1a54456 100644 --- a/tools/phenotype_association/gpass.xml +++ b/tools/phenotype_association/gpass.xml @@ -39,9 +39,9 @@ The input dataset must be in lped_ format, and the output is tabular_. (`Dataset missing?`_) -.. _lped: ./static/formatHelp.html#lped -.. _tabular: ./static/formatHelp.html#tab -.. _Dataset missing?: ./static/formatHelp.html +.. _lped: ${static_path}/formatHelp.html#lped +.. _tabular: ${static_path}/formatHelp.html#tab +.. _Dataset missing?: ${static_path}/formatHelp.html ----- diff --git a/tools/phenotype_association/hilbertvis.xml b/tools/phenotype_association/hilbertvis.xml index 7dccabd2b0a..8a84ff8e656 100644 --- a/tools/phenotype_association/hilbertvis.xml +++ b/tools/phenotype_association/hilbertvis.xml @@ -63,8 +63,8 @@ The input format is interval_, and the output is an image in PDF format. (`Dataset missing?`_) -.. _interval: ./static/formatHelp.html#interval -.. _Dataset missing?: ./static/formatHelp.html +.. _interval: ${static_path}/formatHelp.html#interval +.. _Dataset missing?: ${static_path}/formatHelp.html ----- @@ -75,7 +75,7 @@ position-dependent data. It maps the traditional one-dimensional line visualization onto a two-dimensional square. For example, here is a diagram showing the path of a level-2 Hilbert curve. -.. image:: ./static/images/hilbertvisDiagram.png +.. image:: ${static_path}/images/hilbertvisDiagram.png The shade of each pixel represents the value for the corresponding bin of consecutive genomic positions, calculated according to the specified @@ -99,11 +99,11 @@ Website: http://www.ebi.ac.uk/huber-srv/hilbert/ Here are some examples from the HilbertVis homepage, using ChIP-Seq data. -.. image:: ./static/images/hilbertvis1.png +.. image:: ${static_path}/images/hilbertvis1.png ----- -.. image:: ./static/images/hilbertvis2.png +.. image:: ${static_path}/images/hilbertvis2.png ----- diff --git a/tools/phenotype_association/ldtools.xml b/tools/phenotype_association/ldtools.xml index c3fbe1dc885..86f4f3a1247 100644 --- a/tools/phenotype_association/ldtools.xml +++ b/tools/phenotype_association/ldtools.xml @@ -34,8 +34,8 @@ The input and output datasets are tabular_. (`Dataset missing?`_) -.. _tabular: ./static/formatHelp.html#tab -.. _Dataset missing?: ./static/formatHelp.html +.. _tabular: ${static_path}/formatHelp.html#tab +.. _Dataset missing?: ${static_path}/formatHelp.html ----- diff --git a/tools/phenotype_association/linkToDavid.xml b/tools/phenotype_association/linkToDavid.xml index db34d48a53f..a9574fb8047 100644 --- a/tools/phenotype_association/linkToDavid.xml +++ b/tools/phenotype_association/linkToDavid.xml @@ -76,9 +76,9 @@ The input dataset is in tabular_ format. The output dataset is html_ with a link to the DAVID website as described below. (`Dataset missing?`_) -.. _tabular: ./static/formatHelp.html#tab -.. _html: ./static/formatHelp.html#html -.. _Dataset missing?: ./static/formatHelp.html +.. _tabular: ${static_path}/formatHelp.html#tab +.. _html: ${static_path}/formatHelp.html#html +.. _Dataset missing?: ${static_path}/formatHelp.html ----- diff --git a/tools/phenotype_association/linkToGProfile.xml b/tools/phenotype_association/linkToGProfile.xml index c9b10e266b5..4c5d84bfbd3 100644 --- a/tools/phenotype_association/linkToGProfile.xml +++ b/tools/phenotype_association/linkToGProfile.xml @@ -48,9 +48,9 @@ The input dataset is tabular_ with a column of identifiers. The output dataset is html_ with a link to g:Profiler. (`Dataset missing?`_) -.. _tabular: ./static/formatHelp.html#tab -.. _html: ./static/formatHelp.html#html -.. _Dataset missing?: ./static/formatHelp.html +.. _tabular: ${static_path}/formatHelp.html#tab +.. _html: ${static_path}/formatHelp.html#html +.. _Dataset missing?: ${static_path}/formatHelp.html ----- diff --git a/tools/phenotype_association/lps.xml b/tools/phenotype_association/lps.xml index 3136ebacc01..05bf22ef480 100644 --- a/tools/phenotype_association/lps.xml +++ b/tools/phenotype_association/lps.xml @@ -180,9 +180,9 @@ The input and output datasets are tabular_. The columns are described below. There is a second output dataset (a log) that is in text_ format. (`Dataset missing?`_) -.. _tabular: ./static/formatHelp.html#tab -.. _text: ./static/formatHelp.html#text -.. _Dataset missing?: ./static/formatHelp.html +.. _tabular: ${static_path}/formatHelp.html#tab +.. _text: ${static_path}/formatHelp.html#text +.. _Dataset missing?: ${static_path}/formatHelp.html ----- diff --git a/tools/phenotype_association/pass.xml b/tools/phenotype_association/pass.xml index 959540f7e6d..6d42da95800 100644 --- a/tools/phenotype_association/pass.xml +++ b/tools/phenotype_association/pass.xml @@ -39,9 +39,9 @@ The input is in GFF_ format, and the output is tabular_. (`Dataset missing?`_) -.. _GFF: ./static/formatHelp.html#gff -.. _tabular: ./static/formatHelp.html#tab -.. _Dataset missing?: ./static/formatHelp.html +.. _GFF: ${static_path}/formatHelp.html#gff +.. _tabular: ${static_path}/formatHelp.html#tab +.. _Dataset missing?: ${static_path}/formatHelp.html ----- diff --git a/tools/phenotype_association/sift.xml b/tools/phenotype_association/sift.xml index 5c4f34e8104..b4f3984dd1d 100644 --- a/tools/phenotype_association/sift.xml +++ b/tools/phenotype_association/sift.xml @@ -97,8 +97,8 @@ This currently works only for builds hg18 or hg19. The input and output datasets are tabular_. (`Dataset missing?`_) -.. _tabular: ./static/formatHelp.html#tab -.. _Dataset missing?: ./static/formatHelp.html +.. _tabular: ${static_path}/formatHelp.html#tab +.. _Dataset missing?: ${static_path}/formatHelp.html ----- diff --git a/tools/phenotype_association/snpFreq.xml b/tools/phenotype_association/snpFreq.xml index c06defba07f..df1701a9c55 100644 --- a/tools/phenotype_association/snpFreq.xml +++ b/tools/phenotype_association/snpFreq.xml @@ -44,8 +44,8 @@ The input is tabular_, with six columns of allele counts. The output is also ta and includes all of the input data plus the additional columns described below. (`Dataset missing?`_) -.. _tabular: ./static/formatHelp.html#tab -.. _Dataset missing?: ./static/formatHelp.html +.. _tabular: ${static_path}/formatHelp.html#tab +.. _Dataset missing?: ${static_path}/formatHelp.html ----- diff --git a/tools/plotting/bar_chart.xml b/tools/plotting/bar_chart.xml index ef52b5348f4..b68e7c317b2 100644 --- a/tools/plotting/bar_chart.xml +++ b/tools/plotting/bar_chart.xml @@ -52,7 +52,7 @@ This tool builds a bar chart on one or more columns. Suppose you have dataset li Graphing columns 2 and 3 while using column 1 for X Tick Labels will produce the following plot: -.. image:: ./static/images/bar_chart.png +.. image:: ${static_path}/images/bar_chart.png :height: 324 :width: 540 diff --git a/tools/plotting/boxplot.xml b/tools/plotting/boxplot.xml index 6a97c5191f2..d34c1259bb6 100644 --- a/tools/plotting/boxplot.xml +++ b/tools/plotting/boxplot.xml @@ -95,7 +95,7 @@ Creates a boxplot graph. Its main purpose is to display a distribution of qualit * Rectangular red boxes show the Inter-quartile Range (IQR) (top value is Q3, bottom value is Q1) * Whiskers show outliers at max. 1.5*IQR -.. image:: ./static/images/solid_qual.png +.. image:: ${static_path}/images/solid_qual.png ------ diff --git a/tools/plotting/histogram2.xml b/tools/plotting/histogram2.xml index 043704df771..91c8a9f6088 100644 --- a/tools/plotting/histogram2.xml +++ b/tools/plotting/histogram2.xml @@ -70,7 +70,7 @@ This tool computes a histogram of the numerical values in a column of a dataset. - Create a histogram on column 2 of the above dataset. -.. image:: ./static/images/histogram2.png +.. image:: ${static_path}/images/histogram2.png diff --git a/tools/plotting/scatterplot.xml b/tools/plotting/scatterplot.xml index 6f7ad98c615..7e7b7b5f7c8 100644 --- a/tools/plotting/scatterplot.xml +++ b/tools/plotting/scatterplot.xml @@ -65,7 +65,7 @@ This tool creates a simple scatter plot between two variables containing numeric - Create a simple scatterplot between the variables in column 2 and column 3 of the above dataset. -.. image:: ./static/images/scatterplot.png +.. image:: ${static_path}/images/scatterplot.png diff --git a/tools/plotting/xy_plot.xml b/tools/plotting/xy_plot.xml index f242a6874ee..00acdef726c 100644 --- a/tools/plotting/xy_plot.xml +++ b/tools/plotting/xy_plot.xml @@ -143,6 +143,6 @@ Create a two series XY plot on the above data: - Series 1: Red Dashed-Line plot between columns 1 and 2 - Series 2: Blue Circular-Point plot between columns 3 and 2 -.. image:: ./static/images/xy_example.jpg +.. image:: ${static_path}/images/xy_example.jpg diff --git a/tools/regVariation/compute_q_values.xml b/tools/regVariation/compute_q_values.xml index 382a473f450..075b1f090ad 100644 --- a/tools/regVariation/compute_q_values.xml +++ b/tools/regVariation/compute_q_values.xml @@ -141,13 +141,13 @@ Running the program will give the following output:: 0.03115264 0.009750824 1 -.. image:: ./static/operation_icons/p_hist.png +.. image:: ${static_path}/operation_icons/p_hist.png -.. image:: ./static/operation_icons/q_hist.png +.. image:: ${static_path}/operation_icons/q_hist.png -.. image:: ./static/operation_icons/Q_plots.png +.. image:: ${static_path}/operation_icons/Q_plots.png diff --git a/tools/regVariation/draw_stacked_barplots.xml b/tools/regVariation/draw_stacked_barplots.xml index eba88d62e47..c995c734ae4 100644 --- a/tools/regVariation/draw_stacked_barplots.xml +++ b/tools/regVariation/draw_stacked_barplots.xml @@ -52,7 +52,7 @@ Runnig the program will give the following output:: The stacked bars plot representing the data in the input file. -.. image:: ./static/operation_icons/stacked_bars_plot.png +.. image:: ${static_path}/operation_icons/stacked_bars_plot.png diff --git a/tools/rgenetics/rgManQQ.xml b/tools/rgenetics/rgManQQ.xml index 6bd863f0f9f..edbd358721c 100644 --- a/tools/rgenetics/rgManQQ.xml +++ b/tools/rgenetics/rgManQQ.xml @@ -86,7 +86,7 @@ A "Manhattan" plot shows -log10 p values ordered by offset and by chromosome. Re improbable p values are above the red line which is drawn at the Bonferroni FWER control level (0.05/n where n is the number of tests - this is highly conservative for correlated SNPs typical of GWA) -.. image:: ./static/images/Armitagep_manhattan.png +.. image:: ${static_path}/images/Armitagep_manhattan.png A quantile-quantile (QQ) plot is a good way to see systematic departures from the null expectation of uniform p-values from a genomic analysis. If the QQ plot shows departure from the null (ie a uniform 0-1 @@ -94,7 +94,7 @@ distribution), you hope that this will be in the very smallest p-values suggesti interesting results to look at. A log scale will help emphasise departures from the null at low p values more clear -.. image:: ./static/images/Armitagep_qqplot.png +.. image:: ${static_path}/images/Armitagep_qqplot.png ----- diff --git a/tools/rgenetics/rgWebLogo3.xml b/tools/rgenetics/rgWebLogo3.xml index 6d65d1363ce..8c99e37495a 100644 --- a/tools/rgenetics/rgWebLogo3.xml +++ b/tools/rgenetics/rgWebLogo3.xml @@ -106,7 +106,7 @@ it in to this tool. A typical output looks like this -.. image:: ./static/images/rgWebLogo3_test.jpg +.. image:: ${static_path}/images/rgWebLogo3_test.jpg ---- diff --git a/tools/samtools/pileup_parser.xml b/tools/samtools/pileup_parser.xml index 40bc967de88..978c19b6b91 100644 --- a/tools/samtools/pileup_parser.xml +++ b/tools/samtools/pileup_parser.xml @@ -320,7 +320,7 @@ In this mode, the tool only outputs the lines from the input datasets where at l To call all variants (with no restriction by coverage) with quality above phred value of 20, we will need to set the parameters as follows: -.. image:: ./static/images/pileup_parser_help1.png +.. image:: ${static_path}/images/pileup_parser_help1.png Running the tool with these parameters will return:: @@ -336,7 +336,7 @@ Running the tool with these parameters will return:: In addition to calling variants, it is often useful to know the quality adjusted coverage. Running the tool with these parameters: -.. image:: ./static/images/pileup_parser_help2.png +.. image:: ${static_path}/images/pileup_parser_help2.png will report everything from the original file:: @@ -355,7 +355,7 @@ One can use the last column of this dataset to filter out (using Galaxy's **Filt If you set the **Print total number of differences?** to **Yes** the tool will print an additional column with the total number of reads where a devinat base is above the quality threshold. So, seetiing parametrs like this: -.. image:: ./static/images/pileup_parser_help3.png +.. image:: ${static_path}/images/pileup_parser_help3.png will produce this:: @@ -371,7 +371,7 @@ will produce this:: Setting **Print quality and base string?** to **Yes** as shown here: -.. image:: ./static/images/pileup_parser_help4.png +.. image:: ${static_path}/images/pileup_parser_help4.png will produce this:: diff --git a/tools/solid_tools/solid_qual_boxplot.xml b/tools/solid_tools/solid_qual_boxplot.xml index 3082ad1b357..dd3d1dcd93d 100644 --- a/tools/solid_tools/solid_qual_boxplot.xml +++ b/tools/solid_tools/solid_qual_boxplot.xml @@ -29,7 +29,7 @@ Creates a boxplot graph for the quality scores in the library. * Whiskers show outliers at max. 1.5*IQR -.. image:: ./static/images/solid_qual.png +.. image:: ${static_path}/images/solid_qual.png ------ diff --git a/tools/stats/cor.xml b/tools/stats/cor.xml index 0e241806ce7..65f71c6f651 100644 --- a/tools/stats/cor.xml +++ b/tools/stats/cor.xml @@ -47,19 +47,19 @@ This tool computes the matrix of correlation coefficients between numeric column - **Pearson's Correlation** reflects the degree of linear relationship between two variables. It ranges from +1 to -1. A correlation of +1 means that there is a perfect positive linear relationship between variables. The formula for Pearson's correlation is: - .. image:: ./static/images/pearson.png + .. image:: ${static_path}/images/pearson.png where n is the number of items - **Kendall's rank correlation** is used to measure the degree of correspondence between two rankings and assessing the significance of this correspondence. The formula for Kendall's rank correlation is: - .. image:: ./static/images/kendall.png + .. image:: ${static_path}/images/kendall.png where n is the number of items, and P is the sum. - **Spearman's rank correlation** assesses how well an arbitrary monotonic function could describe the relationship between two variables, without making any assumptions about the frequency distribution of the variables. The formula for Spearman's rank correlation is - .. image:: ./static/images/spearman.png + .. image:: ${static_path}/images/spearman.png where D is the difference between the ranks of corresponding values of X and Y, and N is the number of pairs of values. diff --git a/tools/stats/generate_matrix_for_pca_lda.xml b/tools/stats/generate_matrix_for_pca_lda.xml index ad7fb377a0c..9f1e251524c 100644 --- a/tools/stats/generate_matrix_for_pca_lda.xml +++ b/tools/stats/generate_matrix_for_pca_lda.xml @@ -35,12 +35,12 @@ This tool consists of a module to generate a matrix to be used for running the L - Input file (Source file First) -.. image:: ./static/images/tools/lda/first_matrix_generator_example_file.png +.. image:: ${static_path}/images/tools/lda/first_matrix_generator_example_file.png - Input file (Source file Second) -.. image:: ./static/images/tools/lda/second_matrix_generator_example_file.png +.. image:: ${static_path}/images/tools/lda/second_matrix_generator_example_file.png diff --git a/tools/taxonomy/gi2taxonomy.xml b/tools/taxonomy/gi2taxonomy.xml index 68b14821a09..83aeb22a100 100644 --- a/tools/taxonomy/gi2taxonomy.xml +++ b/tools/taxonomy/gi2taxonomy.xml @@ -50,7 +50,7 @@ Suppose you have BLAST output that looks like this:: and you want to obtain full taxonomic representation for GIs listed in *targetGI* column. If you set parameters as shown here: -.. image:: ./static/images/fetchTax.png +.. image:: ${static_path}/images/fetchTax.png the tool will generate the following output (you may need to scroll sideways to see the entire line):: diff --git a/tools/taxonomy/poisson2test.xml b/tools/taxonomy/poisson2test.xml index bd1cdf5b3df..6907211dbba 100644 --- a/tools/taxonomy/poisson2test.xml +++ b/tools/taxonomy/poisson2test.xml @@ -48,12 +48,12 @@ This utility performs this analysis. It assumes that the data comes from a Poiss Equation 1: -.. image:: ./static/images/poisson2test_eqn1.png +.. image:: ${static_path}/images/poisson2test_eqn1.png Equation 2: -.. image:: ./static/images/poisson2test_eqn2.png +.. image:: ${static_path}/images/poisson2test_eqn2.png X = number of reads falling in a particular taxon in location 1 diff --git a/tools/taxonomy/t2ps_wrapper.xml b/tools/taxonomy/t2ps_wrapper.xml index e2c63b175fb..533fb0670a0 100644 --- a/tools/taxonomy/t2ps_wrapper.xml +++ b/tools/taxonomy/t2ps_wrapper.xml @@ -62,14 +62,14 @@ Suppose you have the following dataset:: Drawing the tree with default parameters (without changing anything in the interface) will produce this tree: -.. image:: ./static/images/t2ps_ideal.png +.. image:: ${static_path}/images/t2ps_ideal.png :width: 500 (for explanation of colors and numbers on the tree scroll to the bottom of this help section) Here *Class* rank represent terminal nodes (leaves) of the tree because it is the default setting of the "*show ranks from root to*" drop-down. Changing the drop-down to "*Subspecies*" will produce this: -.. image:: ./static/images/t2ps_ideal_ssp.png +.. image:: ${static_path}/images/t2ps_ideal_ssp.png :width: 1000 -------- @@ -87,7 +87,7 @@ Real taxonomic datasets almost always contain empty nodes. These are represente A full tree for this dataset will look like this: -.. image:: ./static/images/t2ps_missing_nodes.png +.. image:: ${static_path}/images/t2ps_missing_nodes.png :width: 1000 Missing nodes are simply omitted from the tree (there are no gray boxes corresponding to "n") but the branch length is maintained so that taxa belonging to the same taxonomic rank are always aligned with each other @@ -98,11 +98,11 @@ Missing nodes are simply omitted from the tree (there are no gray boxes correspo You can use the "*maximum number of leaves*" to restrict the tree to a specified number of leaves (external nodes). Using the following setting on the above dataset (note *show ranks from root to* set to *show entire tree* and *maximum number of leaves* is set *3*): -.. image:: ./static/images/t2ps_autoscale.png +.. image:: ${static_path}/images/t2ps_autoscale.png will produce this tree: -.. image:: ./static/images/t2ps_autoscale_tree.png +.. image:: ${static_path}/images/t2ps_autoscale_tree.png :width: 1000 Here the tree is automatically trimmed at a taxonomic rank that will only have 3 outer nodes. This is very useful for initial evaluation of very large trees where you want to only see, say, 1,000 outer nodes at once. @@ -113,11 +113,11 @@ Here the tree is automatically trimmed at a taxonomic rank that will only have 3 Branches of the tree are colored according to the heatmap below. The "bluer" the branch the lesser the number of leaves it leads to and vice versa. -.. image:: ./static/images/t2ps_heatmap.png +.. image:: ${static_path}/images/t2ps_heatmap.png Each node is labeled with taxonomic name and the number of tree leaves belonging to this taxonomic group: -.. image:: ./static/images/t2ps_node_label.png +.. image:: ${static_path}/images/t2ps_node_label.png