diff --git a/tools/discreteWavelet/execute_dwt_IvC_all.xml b/tools/discreteWavelet/execute_dwt_IvC_all.xml index d1dec5d961d..fb048e582bb 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/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 diff --git a/tools/discreteWavelet/execute_dwt_cor_aVa_perClass.xml b/tools/discreteWavelet/execute_dwt_cor_aVa_perClass.xml index 04f24135c11..23c90b4b035 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/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 diff --git a/tools/discreteWavelet/execute_dwt_cor_aVb_all.xml b/tools/discreteWavelet/execute_dwt_cor_aVb_all.xml index 20ac028e802..99147015a84 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/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 diff --git a/tools/discreteWavelet/execute_dwt_var_perClass.xml b/tools/discreteWavelet/execute_dwt_var_perClass.xml index d38c185327e..22fa0ad6257 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/operation_icons/dwt_var_perClass.png diff --git a/tools/emboss_5/emboss_isochore.xml b/tools/emboss_5/emboss_isochore.xml index acf51a9d779..7cbf1e8544e 100644 --- a/tools/emboss_5/emboss_isochore.xml +++ b/tools/emboss_5/emboss_isochore.xml @@ -1,22 +1,22 @@ - - Plots isochores in large DNA sequences - emboss + + Plots isochores in large DNA sequences + emboss emboss_single_outputfile_wrapper.pl isochore -sequence $input1 -outfile $ofile2 -goutfile $ofile1 -graph png -window $window -shift $shift -auto - - - - - - - - - - - - - + + + + + + + + + + + + + - + + --> .. class:: warningmark @@ -76,7 +76,7 @@ This application plots GC content over a sequence. It is intended for large sequ - Output graphics file: -.. image:: ../static/emboss_icons/isochore.png +.. image:: ./static/emboss_icons/isochore.png diff --git a/tools/fastx_toolkit/fastq_quality_boxplot.xml b/tools/fastx_toolkit/fastq_quality_boxplot.xml index fa8363c5b3b..14241b39285 100644 --- a/tools/fastx_toolkit/fastq_quality_boxplot.xml +++ b/tools/fastx_toolkit/fastq_quality_boxplot.xml @@ -1,6 +1,6 @@ - fastx_toolkit + fastx_toolkit fastq_quality_boxplot_graph.sh -t '$input.name' -i $input -o $output @@ -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/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/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/fastx_icons/fastq_quality_boxplot_3.png ------ diff --git a/tools/human_genome_variation/hilbertvis.xml b/tools/human_genome_variation/hilbertvis.xml index 15632915615..7dccabd2b0a 100644 --- a/tools/human_genome_variation/hilbertvis.xml +++ b/tools/human_genome_variation/hilbertvis.xml @@ -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/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/images/hilbertvis1.png ----- -.. image:: ../static/images/hilbertvis2.png +.. image:: ./static/images/hilbertvis2.png ----- diff --git a/tools/maf/interval2maf.xml b/tools/maf/interval2maf.xml index eaf6f9c8689..17c558be6ef 100644 --- a/tools/maf/interval2maf.xml +++ b/tools/maf/interval2maf.xml @@ -3,9 +3,9 @@ #if $maf_source_type.maf_source == "user" #interval2maf.py --dbkey=${input1.dbkey} --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafFile=$maf_source_type.mafFile --mafIndex=$maf_source_type.mafFile.metadata.maf_index --interval_file=$input1 --output_file=$out_file1 --mafIndexFile=${GALAXY_DATA_INDEX_DIR}/maf_index.loc --species=$maf_source_type.species #else #interval2maf.py --dbkey=${input1.dbkey} --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafType=$maf_source_type.mafType --interval_file=$input1 --output_file=$out_file1 --mafIndexFile=${GALAXY_DATA_INDEX_DIR}/maf_index.loc --species=$maf_source_type.species - #end if# --split_blocks_by_species=$split_blocks_by_species_selector.split_blocks_by_species - #if $split_blocks_by_species_selector.split_blocks_by_species == "split_blocks_by_species"# - --remove_all_gap_columns=$split_blocks_by_species_selector.remove_all_gap_columns + #end if# --split_blocks_by_species=$split_blocks_by_species_selector.split_blocks_by_species + #if $split_blocks_by_species_selector.split_blocks_by_species == "split_blocks_by_species"# + --remove_all_gap_columns=$split_blocks_by_species_selector.remove_all_gap_columns #end if @@ -32,13 +32,13 @@ - - + --> @@ -53,22 +53,22 @@ - + - + - + - - + + @@ -79,7 +79,7 @@ - + @@ -87,7 +87,7 @@ - + @@ -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/images/maf_icons/interval2maf.png diff --git a/tools/maf/interval2maf_pairwise.xml b/tools/maf/interval2maf_pairwise.xml index b4270840c3e..230902cce88 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/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 5457717aeb3..d580292c9de 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/images/maf_icons/stitchMaf.png diff --git a/tools/metag_tools/blat_mapping.xml b/tools/metag_tools/blat_mapping.xml index 57c9f18dc01..1af82c3149a 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/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 d6963bac368..ddcbcf93975 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/images/dualcolorcode.png diff --git a/tools/metag_tools/short_reads_figure_score.xml b/tools/metag_tools/short_reads_figure_score.xml index c2ceb24aff0..8b791c8e905 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/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 01c897e1940..90ae83fcfe9 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/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/cluster.xml b/tools/new_operations/cluster.xml index 52c4e71917c..c281cc89ee3 100644 --- a/tools/new_operations/cluster.xml +++ b/tools/new_operations/cluster.xml @@ -83,7 +83,7 @@ See Galaxy Interval Operation Screencasts_ (right click to open this link in ano **Example** -.. image:: ../static/operation_icons/gops_cluster.gif +.. image:: ./static/operation_icons/gops_cluster.gif \ No newline at end of file diff --git a/tools/new_operations/complement.xml b/tools/new_operations/complement.xml index 49b56e3241a..2fcabc6ede6 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/operation_icons/gops_complement.gif diff --git a/tools/new_operations/concat.xml b/tools/new_operations/concat.xml index e2099fb5e9c..118c355e7b7 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/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 0a0ed359363..1c9cb4d29b7 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/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/operation_icons/flanks_ex2.gif diff --git a/tools/new_operations/intersect.xml b/tools/new_operations/intersect.xml index cb1d2b57c8a..cbcd4e7d029 100644 --- a/tools/new_operations/intersect.xml +++ b/tools/new_operations/intersect.xml @@ -132,7 +132,7 @@ See Galaxy Interval Operation Screencasts_ (right click to open this link in ano **Example** -.. image:: ../static/operation_icons/gops_intersect.gif +.. image:: ./static/operation_icons/gops_intersect.gif \ No newline at end of file diff --git a/tools/new_operations/merge.xml b/tools/new_operations/merge.xml index a2925610551..ae7af11fe10 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/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 3036fded636..4e65463b539 100644 --- a/tools/new_operations/subtract.xml +++ b/tools/new_operations/subtract.xml @@ -112,7 +112,7 @@ See Galaxy Interval Operation Screencasts_ (right click to open this link in ano **Example** -.. image:: ../static/operation_icons/gops_subtract.gif +.. image:: ./static/operation_icons/gops_subtract.gif \ No newline at end of file diff --git a/tools/ngs_simulation/ngs_simulation.xml b/tools/ngs_simulation/ngs_simulation.xml index 640365dbd01..e5ea55e8372 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/images/ngs_simulation.png Summary output (txt):: diff --git a/tools/plotting/bar_chart.xml b/tools/plotting/bar_chart.xml index aacc4d9d586..65307f44d5e 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/images/bar_chart.png :height: 324 :width: 540 diff --git a/tools/plotting/boxplot.xml b/tools/plotting/boxplot.xml index 7660572ea7f..ef8a35bb07e 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/images/solid_qual.png diff --git a/tools/plotting/histogram2.xml b/tools/plotting/histogram2.xml index da58044fd5d..6b072458518 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 query. - Create a histogram on column 2 of the above dataset. -.. image:: ../static/images/histogram2.png +.. image:: ./static/images/histogram2.png diff --git a/tools/plotting/scatterplot.xml b/tools/plotting/scatterplot.xml index 32b903bc31c..774847f9943 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/images/scatterplot.png diff --git a/tools/plotting/xy_plot.xml b/tools/plotting/xy_plot.xml index 01fc4ed4b7f..f242a6874ee 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/images/xy_example.jpg diff --git a/tools/regVariation/compute_q_values.xml b/tools/regVariation/compute_q_values.xml index d134bbf5b7b..9ecc7003a73 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/operation_icons/p_hist.png -.. image:: ../static/operation_icons/q_hist.png +.. image:: ./static/operation_icons/q_hist.png -.. image:: ../static/operation_icons/Q_plots.png +.. image:: ./static/operation_icons/Q_plots.png diff --git a/tools/regVariation/draw_stacked_barplots.xml b/tools/regVariation/draw_stacked_barplots.xml index 7923df17b96..a6384f057e5 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/operation_icons/stacked_bars_plot.png diff --git a/tools/rgenetics/rgManQQ.xml b/tools/rgenetics/rgManQQ.xml index 57805e9541f..dca9bc2a11c 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/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/images/Armitagep_qqplot.png ----- diff --git a/tools/rgenetics/rgfakePhe.py b/tools/rgenetics/rgfakePhe.py index 934672d634c..1e60d59286e 100644 --- a/tools/rgenetics/rgfakePhe.py +++ b/tools/rgenetics/rgfakePhe.py @@ -170,7 +170,7 @@ 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/images/xy_example.jpg diff --git a/tools/samtools/pileup_parser.xml b/tools/samtools/pileup_parser.xml index b4ae5fcf8cf..40bc967de88 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/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/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/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/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 8fc5dabcd74..3082ad1b357 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/images/solid_qual.png ------ diff --git a/tools/stats/cor.xml b/tools/stats/cor.xml index 1458a8dd39f..74777436a4b 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/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/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/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 520188744d1..ad7fb377a0c 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/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/images/tools/lda/second_matrix_generator_example_file.png diff --git a/tools/stats/gsummary.xml.groups b/tools/stats/gsummary.xml.groups index fc200b6dac9..8e625040e3c 100644 --- a/tools/stats/gsummary.xml.groups +++ b/tools/stats/gsummary.xml.groups @@ -33,7 +33,7 @@ This tool computes basic summary statistics on a given column, or on an expressi + **c1** *group by the values in column 1* + **c1,c4** *group by the values in column 1, then by the values in column 4* - + ----- **Expression examples** @@ -56,7 +56,7 @@ This tool computes basic summary statistics on a given column, or on an expressi Currently, these R functions are supported: *abs, sign, sqrt, floor, ceiling, trunc, round, signif, exp, log, cos, sin, tan, acos, asin, atan, cosh, sinh, tanh, acosh, asinh, atanh, lgamma, gamma, gammaCody, digamma, trigamma, cumsum, cumprod, cummax, cummin* -.. |INFO| image:: ../static/images/icon_info_sml.gif +.. |INFO| image:: ./static/images/icon_info_sml.gif diff --git a/tools/taxonomy/gi2taxonomy.xml b/tools/taxonomy/gi2taxonomy.xml index fa95eec2729..68b14821a09 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/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 dbd5145a546..bd1cdf5b3df 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/images/poisson2test_eqn1.png Equation 2: -.. image:: ../static/images/poisson2test_eqn2.png +.. image:: ./static/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 a923641b47f..e2c63b175fb 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/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/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/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/images/t2ps_autoscale.png will produce this tree: -.. image:: ../static/images/t2ps_autoscale_tree.png +.. image:: ./static/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/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/images/t2ps_node_label.png