diff plotly_blast_tool/plotlyblast.xml @ 8:186734f1d63c draft default tip

Replace plotly_blast_tool content with blasttools_search. :(

--- a/plotly_blast_tool/plotlyblast.xml	Fri Aug 04 01:52:13 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,279 +0,0 @@
-<tool name="plotlyblast" id="plotlyblast" version="3.0">
-  <!--Source in git at: https://github.com/fubar2/galaxy_tf_overlay-->
-  <!--Created by [e-mail] at 04/08/2023 10:36:02 using the Galaxy Tool Factory.-->
-  <description>Plotly plot generator specialised for 25 column Galaxy blast search result tabular files</description>
-  <requirements>
-    <requirement version="1.5.3" type="package">pandas</requirement>
-    <requirement version="5.9.0" type="package">plotly</requirement>
-    <requirement version="0.2.1" type="package">python-kaleido</requirement>
-  </requirements>
-  <stdio>
-    <exit_code range="1:" level="fatal"/>
-  </stdio>
-  <version_command><![CDATA[echo "3.0"]]></version_command>
-  <command><![CDATA[python
-$runme
---input_tab
-$input_tab
---htmlout
-$htmlout
---xcol
-"$xcol"
---ycol
-"$ycol"
---colourcol
-"$colourcol"
---hovercol
-"$hovercol"
---title
-"$title"
---header
-"$header"
---image_type
-"$outputimagetype"]]></command>
-  <configfiles>
-    <configfile name="runme"><![CDATA[#raw
-
-import argparse
-import shutil
-import sys
-import math
-import plotly.express as px
-import pandas as pd
-# Ross Lazarus July 2023
-# based on various plotly tutorials
-# Expects a blastn search result passed in as the first command line parameter.
-parser = argparse.ArgumentParser()
-a = parser.add_argument
-a('--input_tab',default='')
-a('--header',default='qaccver,saccver,piden,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,sallseqid,score,nident,positive,gaps,ppos,qframe,sframe,qseq,sseq,qlen,slen,salltitles')
-a('--htmlout',default="test_run.html")
-a('--xcol',default='')
-a('--ycol',default='')
-a('--colourcol',default='')
-a('--hovercol',default='')
-a('--title',default='test blast plot')
-a('--image_type',default='short_html')
-args = parser.parse_args()
-df = pd.read_csv(args.input_tab, sep='\t')
-NCOLS = df.columns.size
-MAXLEN = 30 # tricky way to truncate long axis tickmarks
-defaultcols = ['col%d' % (x+1) for x in range(NCOLS)]
-if len(args.header.strip()) > 0:
-    newcols = args.header.split(',')
-    if len(newcols) == NCOLS:
-        df.columns = newcols
-    else:
-        sys.stderr.write('#### Supplied header %s has %d comma delimited header names - does not match the input tabular file %d columns - using col1,...coln' % (args.header, len(newcols), NCOLS))
-        df.columns = defaultcols
-else:
-    df.columns = defaultcols
-df['evalue'] = [-math.log(x + 1e-308) for x in df['evalue']] # convert so large values reflect statistical surprise
-if len(args.colourcol.strip()) == 0:
-    fig = px.scatter(df, x=args.xcol, y=args.ycol, hover_name=args.hovercol)
-else:
-    fig = px.scatter(df, x=args.xcol, y=args.ycol, color=args.colourcol, hover_name=args.hovercol)
-if args.title:
-    ftitle=dict(text=args.title, font=dict(size=40))
-    fig.update_layout(title=ftitle)
-for scatter in fig.data:
-    scatter['x'] = [str(x)[:MAXLEN] + '..' if len(str(x)) > MAXLEN else x for x in scatter['x']]
-    scatter['y'] = [str(x)[:MAXLEN] + '..' if len(str(x)) > MAXLEN else x for x in scatter['y']]
-    if len(args.colourcol.strip()) == 0:
-        sl = str(scatter['legendgroup'])
-        if len(sl) > MAXLEN:
-            scatter['legendgroup'] = sl[:MAXLEN]
-if args.image_type == "short_html":
-    fig.write_html(args.htmlout, full_html=False, include_plotlyjs='cdn')
-elif args.image_type == "long_html":
-    fig.write_html(args.htmlout)
-elif args.image_type == "small_png":
-    ht = 768
-    wdth = 1024
-    fig.write_image('plotly.png', height=ht, width=wdth)
-    shutil.copyfile('plotly.png', args.htmlout)
-else:
-    ht = 1200
-    wdth = 1920
-    fig.write_image('plotly.png', height=ht, width=wdth)
-    shutil.copyfile('plotly.png', args.htmlout)
-
-
-
-#end raw]]></configfile>
-  </configfiles>
-  <inputs>
-    <param name="input_tab" type="data" optional="false" label="Tabular input file to plot" help="" format="tabular" multiple="false"/>
-    <param name="xcol" type="text" value="qaccver" label="x axis for plot" help=""/>
-    <param name="ycol" type="text" value="bitscore" label="y axis for plot" help=""/>
-    <param name="colourcol" type="text" value="piden" label="column containing a groupable variable for colour. Default none." help="Adds a legend so choose wisely "/>
-    <param name="hovercol" type="text" value="qseq" label="columname for hover string" help=""/>
-    <param name="title" type="text" value="Qaccver by bitscore coloured by pident. Hover shows blast match." label="Title for the plot" help="Special characters will probably be escaped so do not use them"/>
-    <param name="header" type="text" value="qaccver,saccver,piden,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,sallseqid,score,nident,positive,gaps,ppos,qframe,sframe,qseq,sseq,qlen,slen,salltitles" label="Use this comma delimited list of column header names for this tabular file. Default is None when col1...coln will be used" help="Default for Galaxy blast outputs with 25 columns. The column names supplied for xcol, ycol, hover and colour MUST match either the supplied list, or if none, col1...coln."/>
-    <param name="outputimagetype" type="select" label="Select the output format for this plot image" help="Small and large png are not interactive but best for many (__gt__10k) points. Stand-alone HTML includes 3MB of javascript. Short form HTML gets it the usual way so can be cut and paste into documents.">
-      <option value="short_html">Short HTML interactive - requires network connection to download 3MB javascript</option>
-      <option value="long_html">Long HTML for stand-alone viewing where network access to libraries is not available.</option>
-      <option value="large_png">Large (1920x1200) png image - not interactive so hover column ignored</option>
-      <option value="small_png">Small (1024x768) png image - not interactive so hover column ignored</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data name="htmlout" format="html" label="Plotlyblast $title on $input_tab.element_identifier" hidden="false">
-      <change_format>
-        <when input="outputimagetype" format="png" value="small_png"/>
-        <when input="outputimagetype" format="png" value="large_png"/>
-      </change_format>
-    </data>
-  </outputs>
-  <tests>
-    <test>
-      <output name="htmlout" value="htmlout_sample" compare="sim_size" delta="5000"/>
-      <param name="input_tab" value="input_tab_sample"/>
-      <param name="xcol" value="qaccver"/>
-      <param name="ycol" value="bitscore"/>
-      <param name="colourcol" value="piden"/>
-      <param name="hovercol" value="qseq"/>
-      <param name="title" value="Qaccver by bitscore coloured by pident. Hover shows blast match."/>
-      <param name="header" value="qaccver,saccver,piden,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,sallseqid,score,nident,positive,gaps,ppos,qframe,sframe,qseq,sseq,qlen,slen,salltitles"/>
-      <param name="outputimagetype" value="short_html"/>
-    </test>
-  </tests>
-  <help><![CDATA[
-
-This is a specialised version of a generic tabular file plotter tool plotlytabular
-
-PNG image outputs are not interactive but best for very large numbers of data points. Hover column will be ignored.
-
-HTML interactive plots are best for a few thousand data points at most because
-
-the hover information becomes uncontrollable with very dense points.
-
-Using the shorter format HTML relies on internet access when viewed, and saves 3MB of javascript being embedded.
-
-The long format is useful if potentially viewed offline.
-
-
-
-.. class:: warningmark
-
-NOTE: Long strings in x and y tickmarks WILL BE TRUNCATED if they are too long - ".." is added to indicate truncation - otherwise some plots are squished.
-
-
-
-.. class:: warningmark
-
-NOTE: Blast evalues WILL BE TRANSFORMED using -log10(evalue), so they are scaled in a way that doesn't confuse plotly.express with the tiny values.
-
-
-
-----
-
-
-
-The main reason to run this tool is to have an interactive hover text specified so it appears when hovering over each data point to supply useful information. 
-
-
-
-Assumes you want a hover display for an interactive plot to be informative
-
-
-
-Column names are auto-generated as col1,...coln unless a comma separated list of column names is supplied as the header parameter.
-
-
-
-For example, using a Galaxy blastn output with 25 columns, the following comma delimited string supplied as the "header" parameter will match the names of each column.
-
-   qaccver,saccver,piden,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,sallseqid,score,nident,positive,gaps,ppos,qframe,sframe,qseq,sseq,qlen,slen,salltitles
-
-
-
-When a header is supplied, the xcol and other column names must match one of those supplied column names.
-
-So for example, xcol = "qaccver" for the blastn header example rather than xcol = "col1" when no header is supplied.
-
-
-
-Relies on Plotly python code released under the MIT licence: https://github.com/plotly/plotly.py/blob/master/LICENSE.txt
-
-
-
-
-
- 
-
-------
-
-
-Script::
-
-    import argparse
-    import shutil
-    import sys
-    import math
-    import plotly.express as px
-    import pandas as pd
-    # Ross Lazarus July 2023
-    # based on various plotly tutorials
-    # Expects a blastn search result passed in as the first command line parameter.
-    parser = argparse.ArgumentParser()
-    a = parser.add_argument
-    a('--input_tab',default='')
-    a('--header',default='qaccver,saccver,piden,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,sallseqid,score,nident,positive,gaps,ppos,qframe,sframe,qseq,sseq,qlen,slen,salltitles')
-    a('--htmlout',default="test_run.html")
-    a('--xcol',default='')
-    a('--ycol',default='')
-    a('--colourcol',default='')
-    a('--hovercol',default='')
-    a('--title',default='test blast plot')
-    a('--image_type',default='short_html')
-    args = parser.parse_args()
-    df = pd.read_csv(args.input_tab, sep='\t')
-    NCOLS = df.columns.size
-    MAXLEN = 30 # tricky way to truncate long axis tickmarks
-    defaultcols = ['col%d' % (x+1) for x in range(NCOLS)]
-    if len(args.header.strip()) > 0:
-        newcols = args.header.split(',')
-        if len(newcols) == NCOLS:
-            df.columns = newcols
-        else:
-            sys.stderr.write('#### Supplied header %s has %d comma delimited header names - does not match the input tabular file %d columns - using col1,...coln' % (args.header, len(newcols), NCOLS))
-            df.columns = defaultcols
-    else:
-        df.columns = defaultcols
-    df['evalue'] = [-math.log(x + 1e-308) for x in df['evalue']] # convert so large values reflect statistical surprise
-    if len(args.colourcol.strip()) == 0:
-        fig = px.scatter(df, x=args.xcol, y=args.ycol, hover_name=args.hovercol)
-    else:
-        fig = px.scatter(df, x=args.xcol, y=args.ycol, color=args.colourcol, hover_name=args.hovercol)
-    if args.title:
-        ftitle=dict(text=args.title, font=dict(size=40))
-        fig.update_layout(title=ftitle)
-    for scatter in fig.data:
-        scatter['x'] = [str(x)[:MAXLEN] + '..' if len(str(x)) > MAXLEN else x for x in scatter['x']]
-        scatter['y'] = [str(x)[:MAXLEN] + '..' if len(str(x)) > MAXLEN else x for x in scatter['y']]
-        if len(args.colourcol.strip()) == 0:
-            sl = str(scatter['legendgroup'])
-            if len(sl) > MAXLEN:
-                scatter['legendgroup'] = sl[:MAXLEN]
-    if args.image_type == "short_html":
-        fig.write_html(args.htmlout, full_html=False, include_plotlyjs='cdn')
-    elif args.image_type == "long_html":
-        fig.write_html(args.htmlout)
-    elif args.image_type == "small_png":
-        ht = 768
-        wdth = 1024
-        fig.write_image('plotly.png', height=ht, width=wdth)
-        shutil.copyfile('plotly.png', args.htmlout)
-    else:
-        ht = 1200
-        wdth = 1920
-        fig.write_image('plotly.png', height=ht, width=wdth)
-        shutil.copyfile('plotly.png', args.htmlout)
-
-]]></help>
-  <citations>
-    <citation type="doi">10.1093/bioinformatics/bts573</citation>
-  </citations>
-</tool>
-